Spoiler Best/Worst Final Dungeons - (a ranked list)

[Iridescence]

1. Sky Keep (SS) - One thing that's missing is the boss itself, though the apple didn't fall too far from the tree. It had lots of color, variety, and the dungeon itself was a puzzle. Loved it.
2. Tower of Ganon (ALTTP) - Actions, bosses, puzzles. This one has it all.
3. Level 9 (LOZ) - Was the half the size of the entire overworld combined. The other dungeons were simple, but this one was by far the most cerebral and difficult.
4. Ganon's Castle (OOT) - Gives you a smorgasbord of different puzzles in different rooms and a great finale.
5. Dark Hyrule Castle (TMC) - Nice darkish atmosphere. Kinda borrows from ALTTP, but has its own nice twist to it. All around fun.
6. Hyrule Castle (TP) - Not the best dungeon in TP and the bosses were underwhelming, but the atmosphere was certainly there and it was full of various puzzles.
   
7. Lorule Castle (ALBW) - It's segmented and by the numbers, but the elements themselves in it are good.
8. Ganon's Tower (TWW) - It's like a stripped down version of OOT's final dungeon. The level design is so bad here. This was rushed, but it did have good bosses and an epic finale.
9. The Moon (MM) - Nice atmosphere, story, some mini-dungeons, and the Majora battles, but not quite a dungeon.
   
10. Wind Fish Egg (LA) - "Lost Wood" esque puzzles are stupid, but a great string of boss fights help.
11. Black Tower (OOA) - Was really short, but the warping and light puzzle elements were kinda cool.
12. Room of Rites (OOX) - The eyes concept and the boss battles were good, but way too short.
    
13. Onox's Castle (OOS) - Cool dragon boss, but could a dungeon be any lazier and more perfunctory?

Overall Thoughts

1. In ranking them, I considered the boss fights as a factor, but I graded them as dungeons first, so level design and atmosphere matter more
2. The final dungeons in Zelda games tend to be far from the best in their respective games.
3. It's possible that time constraints make the last dungeons rushed.
4. Or it's also possible that by the end, the player just wants to fight the boss (and navigating through a large dungeon may ruin the moment)
5. I excluded PH/ST (hub-dungeons aren't fair game) and AOL/FS/FSA for not having conventional dungeons.

 

[DarkestLink]

Throwing this out there, I don't consider the Moon to even be a dungeon, so it's not included.

1) Ganon's Tower: Nice varied amount of puzzles, and some good combat towards the end. Very climatic.
2) Hyrule Castle: Perfect size, good combat, but have used more puzzles and not very climatic towards the beginning.
3) Lorule Castle: Very climatic, good length, but the puzzles were very easy. The combat was OK.
4) Ganon's Tower: Wasn't a fan of the bosses in tWW, so that really dragged this down for me, but it felt fairly climatic and the puzzles were decent.
5) Tower of Spirits: Amazing puzzles and good combat. Length was fine, but it didn't feel climatic.
6) Sky Keep: Had good puzzles, and OK combat, but it felt very anticlimatic, involved a lot of waiting, and was a little too short overall.
7) Black Tower: Really short, but at least it felt climatic.
8) Temple of the Ocean King: Felt kinda...dull the umpteenth time around.
9) The various dungeons I don't remember (AoL, LA, FSA, and MC)
13) Level 9: Took waaaaay too long. No real puzzles in the game to begin with. Combat was....OK. No real story for it to feel "climatic".
14) Tower of Ganon: The absolute worst. Halfway through, I wasn't even hyped for the final fight anymore. I was just checking my watch and wondering when it'd be over with. Like LoZ, there were no puzzles to be had or a story to be hyped up for. The combat in the game in general was just meh. And this dungeon just really dragged it out...

EDIT: Looking back, ToG wasn't NEARLY as long as I thought it was....it just felt that way. After getting out, I felt I had spent two hours in there.

 

[ReveredPartisan]

There are a few different approaches you can take here: you can go aLttP's route with a monolithic hyper-dungeon where all of your questing culminates in one final challenge, or you could go the way of TP, where a brief but deeply atmospheric challenge hypes you for the final battle; depends on the nature of the game, I suppose. Hyrule Castle would have been underwhelming in ALttP, and the Tower of Ganon would have felt out of place in TP. Ultimately, there really aren't many parallels between them, and consequently, I'd argue it's out of place to judge them on a spectrum.

 

[PhantomTriforce]

1. Ganon's Tower (ALttP) - This dungeon is perfect in every way. It gave me a very tough final challenge, and it should be the standard for what a final dungeon in a Zelda game should be. If there is one thing that I look the most forward to in every ALttP run, it is playing this dungeon again.
2. Dark Hyrule Castle - Set a similar kind of hype presented in Ganon's Tower from ALttP, I liked the design of this dungeon, it was very solid overall.
3. Lorule Castle - Like Dark Hyrule Castle, it set a similar kind of hype presented in Ganon's Tower from ALttP, but it wasn't as hard as it should have been.
4. Temple of the Ocean King - idk I enjoyed blasting through this place with my new weapon for the last time.
5. Tower of Spirits - ^
6. Sky Keep - The ultimate puzzle.
7. Ganon's Tower (WW) - Refighting bosses like in ALttP, but they didn't do anything to make the fight harder. Could have been longer.
8. Ganon's Castle (OoT) - It was alright overall, could have been more challenging.
9. Hyrule Castle (TP) - For such an epic game, this was sorta underwhelming, it was very short and not all that tough.
10. Death Mountain - Long and challenging for sure, I just wasn't a fan of this or the rest of the game really.
11. The Black Tower - Set in the location we had been hearing about all game, but it was so short and easy.
12. Onox's Castle - lol but Face miniboss tho
13. The Egg - even more lol
14. Majora's Mask - did this game even have one.
15. Haven't played AoL.