OK, time for my list (it might differ slightly from any previous list in any other thread I've made, but well, I guess opinions change a bit over time). I'll only list the console titles (excluding the Four Swords game(s?) which I've never played and spin-offs) to make comparisons easier for me.
Keep in mind that even if it might sometimes sound like it, I'm not bashing any of the games that are lower on the list, even the lowest one has still a 7/10 rating and was an enjoyable game. I'm just making comparisons between "good", "very good" and "excellent"
I had a lot of fun with all the Zelda games I've played until now (including the handheld ones).
The first place is a tie between aLttP and MM, so I'll just order them chronolgically.
1. A Link to the Past: (10/10)
This game was a great improvement over the original LoZ and introduced very many great things to the series that are still present in modern games (I'm probably even forgetting half of the them):
- the 7 maidens/sages
- the Master Sword
- the general game/story progression which has been present in this or a similar way in all subsequent Ganon(dorf) games (first part with 3 "introductory" dungeons -> Master Sword -> plot twist -> new world/time/situation -> harder dungeons -> final dungeon with Ganon battle)
- multi-floored dungeons with somehow interacting floors (I don't want to count AoL here because of the totally different dungeon concept and the missing depth dimension)
- generally "themed" dungeons like desert/water/forest/ice etc. (also there was the first dungeon with changing water levels, although in a quite primitive way)
- multi-exit/entrance dungeons (where have they gone? :/)
- Link can finally swim
- 1/4 heart pieces
- Fairy upgrades
- Items: Hookshot, hammer (again not counting the one from AoL cause you couldn't freely use it), bottles, Cane of Byrna (kind of like Nayru's Love in OoT/magical armor in WW/TP), super bombs (~powder keg)
- Mirror Shield
- Boss room key
- Places: Hyrule Castle, Kakariko Village, Lake Hylia, Graveyard
- Music: first boss battle music, first Ganon battle music, Ganon's theme, Zelda's Lullaby, Kakariko Village, Hyrule Castle, Getting the Master Sword, File Select Screen/Great Fairy Theme (even if it was somehow borrowed from SMB3)
- (real) minigames
- pots
... and probably many more (subtle) things
Then the difficulty level was just perfect: not crazily hard like AoL but not as easy-peasy as most of its successors.
I also liked that bosses could be beaten in many different ways (you did not have to or sometimes even could not use the respective dungeon item, unlike in most 3D games). They were quite challenging too, and part of the challenge was finding out the weak spot, which was not given away that easily back then.
And it was the last game where you could almost freely shuffle the order in which you played through the dungeons of the game's second part (OoT allowed only a little bit of changing, MM, WW and TP none at all).
Surely, nostalgia value might also play a certain role in the way I look at the game (it was my very first Zelda game), but nevertheless one has to admit that it's an excellent game.
1. Majora's Mask: (10/10)
Here too, I think that it was a great improvement over an earlier similar installment - in this case OoT (more there).
It's an awesome game in all categories, so let's start with the story. It greatly differs from most other Zelda games (there's no "1st part -> MS -> plot twist -> second part -> final battle"-scheme here, as I described it above). Then it has the deepest and darkest story of all the games in the series until now, and the many different and unique characters were well-developed too. I like how things actually change in the game with the days going by: Unlike in most other Zelda games, on a different day the same character will do different things, be in different places and say different things; usually the general mood will get darker the closer you get towards doomsday. This development was implemented very well, as reinforced by the changing weather/environmental effects too: The first day is sunny, Day 2 is rainy and on the final day, the earth shakes and the sky is red, while the moon is slowly coming closer and closer. That and the time limit in general really push the player forward!
Then the gameplay: I really liked how Link could use 4 different shapes, all of them with different abilities and weaknesses and IMO they were all fun to use and you really got to use them a lot, it was executed
much better than the wolf in TP and didn't feel that forced at all. Especially the final battle could be fought using many different shapes and techniques depending on your personal challenge requirements, which made added to the non-linearity, a thing I also liked about aLttP.
I know that many players are quite disappointed by the small number of dungeons. But IMO, I'd rather have few excellent dungeons like in MM than many rather mediocre dungeons (yes I'm looking at
you, OoT). The series has yet to see dungeons again that were so creative, well-designed and rich in variety as the ones in MM, especially Stone Tower Temple, which is by far my #1 favourite dungeon in the series, where you had to use all of your transformation masks, plus the flipping thing was very unique. The bosses, while still relatively easy, were the hardest ones of all 3D Zeldas (I don't know how long it took me to beat Gyorg the first time...).
I also feel that adding in more dungeons would've made the game more boring, IMO it's just perfect the way it is. And people complaining about the number of dungeons should also consider the fact that every dungeon in the game was preceded by some sort of pre-dungeon or at least pre-dungeon action of respectable size. There was the Deku Palace+Koume/Kotake before Woodfall temple, the Goron Baby quest before Snowhead, the Gerudo fortress+Zora hall before Great Bay Temple, and even 2 of them before Stone Tower Temple: Bottom of the Well and Ikana Castle (the latter one with a fairly tough "mini"-boss battle, which was IMO harder than most of OoT's and all of WW/TP's bosses). Then there was the (optional) final dungeon on the moon. Makes 9 dungeons in my definition, that's really OK. And then there are tons of sidequests, which make the game more non-linear, so you can actually "choose" if it's a short game or not. For me at least, it wasn't. It actually took me roughly two times as long to beat as OoT.
The controls were good too, basically the same as in OoT with some updating. Same goes for the graphics which were quite a bit improved compared to OoT, all the areas had their unique feelings to them and were very detailed, especially if considering that the game is over 10 years old now. Though it may be considered a dark game storywise, I think the colours were very powerful, bright and rich in contrast, though (luckily) not as extremely as in WW, again, just right.
Like in most other Zelda games, the music was great. Not too much was re-used from previous games, but the new, IMO sometimes Chinese-themed pieces were just as good and brought in some "fresh wind". Even here, with the Clock Town Theme, the music changed over the days to become more and more hectical, and the theme played in the last 6 hours was the icing of the cake! Especially the Song of Healing/Clock Tower, Ikana Canyon, Ikana Castle, Stone Tower and Great Bay Temple themes are among the most memorable video game tunes for me.
The time limit was crucial to the story, so I think it was OK, plus it added some challenge to the game. Sure, they might have given more hints and made it more obvious to learn about the Inverted/Double Song of Time and that it's important to save and reset time at the owl statues in front of the dungeons, but hey, the game (IMO games in general) isn't supposed to tell you everything and be a cakewalk. After all, puzzles and secrets have always been a big part of the core of the series.
3. Ocarina of Time: (9/10)
The first Zelda in 3D and a great game. It brought Zelda into a new gaming era and was maybe the most revolutionary title in the series. It showed that the transition from 2D to 3D worked well from the start, unlike it was the case with other big game franchises (like Mario (YI->64) and Final Fantasy (VI->VII), but that's my opinion).
There's not much to say about the story, IMO it has very many parallels to aLttP. My theory is that maybe they didn't want to change it that much because the leap to 3D was enough change already and making a totally new story maybe would've repelled gamers, they made their experience with AoL not too long before they started with the development of OoT. With the new cartridge and the extra memory it provided, they could go a bit further in-depth though and thanks to the new hardware they also could show 3D cutscenes, so story-wise I'd say it's an improved and slightly changed version of aLttP (timeline placement, the rise of Ganon etc.), and because I liked aLttP already I'm more than fine with it.
Now the gameplay. With the 2D->3D transition, unkown territory was entered, just like when the first Zelda came out - it hadn't been done before. Keeping that in mind the developers did a really good job. Overall the controls worked well, Z-targeting made its debut and Link responded well to the commands. The overworld was huge with a lot of areas to explore, the dungeons were good overall, although a bit too linear and easy, and the bosses didn't pose much of a challenge, but hey it was the first 3D game and you can't get everything perfect on first try. The forest and water temples are a great exception to that though, they made really good use of the 3D and required some thinking. The only flaw was having to change boots very often in the water temple, but hopefully this will be fixed in the 3DS re-release. The Ganondorf and Ganon battles are among the most epic final boss battles in any video game. But IMO they also should've made the beast Ganon battle a bit harder, while the human Ganondorf battle was OK.
The graphics were top-notch for the time the game came out, especially in the dungeons: Heat wave effects in the Fire Temple, underwater effects, and the Bottom of the Well/Shadow Temple felt really creepy though I played it the first time when I was 20. The only complaint I have here is the emptiness of Hyrule Field, it could've used some more detail, but I guess the 32MB cartridge memory limit stood in the way.
The music in the game reused and popularized many of the older themes (Zelda's Lullaby, Kakariko Village, Ganon's theme...), but also introduced nice new pieces. While the BGM of the first 3 dungeons was rather shallow and bearly noticable, it got a lot better in the adult temples. I especially like the Forest Temple, Fire Temple (1.0) and Spirit Temple themes, but also the Kokiri Forest, Gerudo Valley and Zora's Domain themes.
After all a very good game with some minor forgivable flaws.
4. The Legend of Zelda (NES): (8.5/10)
The beginning of the greatest video game series, this is where it all started. Never before had there been a similar game,
so it was a start from zero.
Typically for the NES games, there isn't much of a story, basically it's just "Save the Princess", an idea that was maybe influenced by the Mario series.
Gameplay was revolutionary back then, instead of fighting your way up from level to level, the player has to explore manually and can play through the dungeons in different orders, get optional upgrades such as stronger swords/shields/armor and heart containers. The non-linearity continues in the dungeons themselves, where instead of going from screen to screen to advance, side rooms have to be visited and mazes to be solved, plus there are hidden objects such as keys, items, movable blocks, bombable/invisible walls etc. The challenge is split between fighting the enemies and solving puzzles. The enemies are quite challenging, especially if you walk into rooms with several blue wizzrobes+bue darknuts+bubbles and maybe even blocks in your way, as it can happen in the final dungeon. The puzzles can become very tedious, especially if bombable walls/burnable bushes are hidden in the overworld (remember that such things are
not indicated by anything, you literally have to burn every bush and bomb every square of rock to find everything, and bomb-dropping enemies are rather rare!). But it's a NES game, and most of them are considered very hard by today's standards, plus it was the very first installment in the series, so the developers didn't have any feedback yet. Nevertheless, I still consider it a good and challenging game (I sometimes wish modern Zelda games would go back a little in that direction instead of being
too obvious with puzzles and having
too weak enemies).
5. Adventure of Link: (8/10)
With the second game in the series, gameplay radically changed from top-view to sidescrolling, plus an RPG-ish level system for magic points, life points and hit strength was installed. There were two different "screen levels", the top-view overworld and a sidescrolling battle/town/dungeon screen. Exploring was still very important, you could easily miss items necessary for progression. Life and magic upgrades were hidden very subtly, the only way to find them all was stepping on every square of the overworld map. The combat difficulty was increased quite a bit compared to LoZ, which still is generally OK to me, because I like some challenge. However, some parts were exaggerated a bit: The blue flying ironknuckles were extremely nasty, and the fact that if you fell into a pit/water(!)/lava = instant death combined with the extreme length of the final dungeon made it a bit too frustrating at some points.
Not much to say about the graphics, I'd say they're pretty standard for NES titles of that time. Later NES titles had much better animations and gfx in general though, for example FFIII(j).
The music, though not composed by Koji Kondo, was good too, especially the two dungeon themes.
5. Twilight Princess: (8/10)
The most recent console title was an enjoyable game too, with excellent graphics and music and good story, but it lacked a bit in challenge.
I personally didn't dislike the story too much, and I can't complain about Ganon being introduced mid-game, but I agree that Zant could've been a bit more badass and shouldn't have been revealed as some kind of psycho towards the end of the game, but that's minor. Midna's character development made up for it.
Now for the gameplay, I like how they improved horse-riding (introduction of horseback combat, Link finally becomes vulnerable while on Epona) and introduced new sword techniques. The dungeon design was OK and introduced many new good ideas, but the problem is that the game is too linear and things are too obvious, especially in the dungeons. There was much potential but it wasn't used to its full extent. Especially the bosses: While physically huge and optically impressive, none of them was anywhere near challenging, the weak spots were too obvious and they didn't really attack you that much. While having some nice battle phases (vs. King Bulbin), the game was a bit too slow-paced. Even in the final battle, there were many 10sec+ idle phases (waiting for Puppet Zelda to charge up the sword, waiting for Beast Ganon to come out of the portals, catching up to horseback Ganon).
So generally spoken, while introducing many nice ideas, they aren't used in the right way, making the game too easy.
Like I said, I really like the graphics of the game a lot. Many people complain that it be "too mature" and/or "too brown", here I must strongly disagree. I don't think it's too photorealisitic, it's just very detailed (doesn't it even partially use cel-shading?) and I don't think it's brown at all. The water is crystal-clear, and especially the Light Spirit Fountains are very colourful and bright (not "brown" at all). OK, the dungeons may be a little dark, but they're dungeons after all, so they're supposed to be a bit darker than the normal overworld, right? And it doesn't even apply to all of them, the Temple of Time is actually very bright, and IMO Arbiter's Grounds, which may be considered TP's darkest dungeon, is still way not as creepy and dark as the Bottom of the Well and Shadow Temple in OoT.
The music of the game was excellent again, with a very huge soundtrack. I think they made the right decision by not using the LoZ theme as overworld theme, because that would spoil it too much (it's OK when it comes back from time to time like in aLttP and MM, but it shouldn't be too often so that it stays enjoyable). I actually liked many songs in the game, out of my head the Field Theme, Snowpeak Ruins Theme, Exterior Twilight Palace Theme, Midna's Desperate Hour, Hidden Village Theme, etc.
7. Wind Waker: (7/10)
This time, let's start right away with the most controversial feature of this game: the graphics. Which are generally a matter of taste, so any general debate about cel-shading or not is quite useless. I generally do not have a problem with cel-shading/cartoonish graphics. In fact, I still like classical cartoons and comics quite a lot. But here's the problem, I usually don't like anime/manga/hentai/anything like that. My biggest problem with the graphics in WW are that all the characters are
totally blown out of proportion. Does Link's Head really have to make up ~50% of his body size and ~90% of his body mass? And eyes bigger than his arms? Even with cartoonish proportions, he looks like 6 years old or younger. Sorry, this is too extreme for me, I just don't like it. Another thing I don't like here are the exaggerated brightness, saturation and contrast of the colours, especially near the beginning of the game. Honestly, it's the only video game I've played where I had to manually tone down these values on my screen to avoid eye cancer. Cel-shading OK, cartoonish characters OK, but there's always a limit. Even if they wanted to make it specially children-friendly, I think it's too much, I don't think kids aged 8 or so really want this extremeness. I played aLttP when I was 7 and many of my friends did back then, and we aren't / never were anything near "emo-kids" or the like, but we still weren't extremely scared/found it too mature or anything like that.
OK enough ranting for now, let's take a look at the story. I think it was one of the better stories in the series, maybe even second to MM. Quite deep and detailed, totally contrasting the graphics. The only disappointment is that Tetra completely disappears after she's revealed as Zelda until the very end of the game.
Now the gameplay: similarly to TP, many new good ideas were introduced (sailing, sword techniques, controlling other characters, even flying) and some of them were actually quite fun to use, but the execution could have been better. Enemies were
way too weak and puzzles
way too easy and obvious, I can't remember many situations in dungeons where I had to stop and think, and I never hads problems getting all the treasure chests. Also, I would've liked to see some better combining use of different items (not necessarily at the same time, but fx in a single puzzle), changing the wind and teleporting lasted too long (unskippable replay of the songs and cutscenes everytime, similar to using the grappling hook), and to reduce the amount of time spent sailing (and mainly only seeing the same blue opaque water all the time) the overworld could've been easily condensed to 50% in both axes and there still would've been more than enough wide open sea. An upgrade for the sail (maybe a "magical sail" that slowly uses magic) would've been cool too. At least there was some use for the giantic amounts of rupees you found in the game - the Tingle decoding (2800 rupees+x), but it felt rather forced, though I didn't have to grind for it. Grandma's soup, bulk quantities of fairies and the fact that you barely got hurt made the rupees somehow obsolete. Needless to say that the bosses were all pushovers and their weak spot was too obvious. Only the final form of Ganondorf deducted some hearts (kicking through the shield defense), IMO that's how hard a normal boss should've been.
The music was one of the rather positive sides of the game, I liked that they made some references to aLttP (Hyrule Castle, Master Sword, Zelda's "appeareance" - aLttP title screen!, Ganon's Theme) and I also liked most of the new songs (here, some seemed to be Celtic-themed) like the overworld theme and the TotG theme (which somehow reminds me of Ikana Castle theme). Only the Outset Island theme sounded a bit too "innocent" and kid-friendly.
After all I still had a good amount of fun playing the game, and even if graphics aren't my main concern in a game, I have to say that they ruined it a bit for me
(BTW I honestly don't believe anyone that claims that "graphics don't matter at all" to him/her, if Link wore a pink kimono and was tatooed all over the face in the next game, you'd be like "WTF" too 
)
Phew, that was >2 hours of writing now, so anyone who actually didn't tl;dr and read through these 21 kilobytes of text wins 5 internets!
