Graphics: Skyward Sword. It has the best graphics from a Zelda game so far. It was more colorful than TP, and the painting effect is quite nice.
Controls: Skyward Sword. With the use of the Motion Plus, the controls of the items and the sword are better than ever. And the The fact that you can choose whichever item you want without pausing the game was a great addition too.
Story: Skyward Sword. I've never been so moved by a story in a video game before SS. The great characters and their development really helped to make the best story in a Zelda game so far.
Music: Ocarina of Time & Majora's Mask. Both of these games have stellar soundtracks, most of the songs are very memorable and fit the areas they are in particularly well.
Combat: Skyward Sword. The enemies in SS are challenging enough, and you really need to think about the direction you slash with your sword, instead of just pressing a button as fast as you can to defeat an enemy. The shield is also more useful than ever before.
Characters: Skyward Sword. Every character has a unique personality in the game, and none of them feel bland, as opposed to other games in the series. The main characters, especially Zelda, Ghirahim, Impa and Groose were particularly great.
Items: Majora's Mask. With the many masks and the more traditional items, I think MM wins this category.
Bosses: Ocarina of Time. Most of the bosses offer a bit of a challenge, and they all require different strategies to defeat them. And they are pretty much all memorable too.
Exploration: Wind Waker. The sense of exploration was very exciting, at least to me, in WW. There are a lot of islands to explore, and you never know what you will encounter during your travels.
Overworld: Ocarina of Time The overworld in OOT was almost perfect. There are many areas, such as forest, mountains, lake, desert, and of course the field. All of them feel connected and aren't too far away from each other. There are many different villages, representing all the different tribes. The areas are all open for a bit of exploration too.
Dungeons: Ocarina of Time & Skyward Sword. OOT features many of the best dungeons in the series, such as the Forest Temple, the Shadow Temple and the Spirit Temple. But all of its dungeons were quite enjoying as they all had a diverse layout, some being more linear, others more opens, etc. With SS, each dungeon is really compact and has its own theme. The Sandship and the Sky Keep were particularly unique and fun to go through. Both of these games's dungeons feature good puzzles too.
Sidequests: Majora's Mask.
Puzzles: Ocarina of Time: Master Quest. I think this one has the most difficult puzzles in the entire series. Even the first dungeon is now challenging. I really scratched my head several times when going through the dungeons in MQ.
Sense of Epicness: Ocarina of Time. The story coupled with the cutscenes makes OOT the most epic Zelda game.
Method of Transport: Wind Waker. Navigating on the Great Sea on the boat with the excellent music and with enemies across your ways makes it my favorite method of transportation in the series. I also liked that you can use your items on the boat in different ways, such as the hook crane or the canon.
Sidekick: Twilight Princess. Midna is the best sidekick I think. She was helpful when needed, and was an interesting character.
Difficulty: A Link to the Past. ALttP has the most balanced difficulty of any Zelda game. Not too hard, not too easy, with a nice learning curve as you progress throughout the game.
Replay Value: Majora's Mask. MM has tons of things to do aside from the main quest, and even after several playthroughs, you can still discover many things (such as the scene with Anju and her mom). You can also refight all the bosses at any time thanks to the 3 day cycle.
Controls: Skyward Sword. With the use of the Motion Plus, the controls of the items and the sword are better than ever. And the The fact that you can choose whichever item you want without pausing the game was a great addition too.
Story: Skyward Sword. I've never been so moved by a story in a video game before SS. The great characters and their development really helped to make the best story in a Zelda game so far.
Music: Ocarina of Time & Majora's Mask. Both of these games have stellar soundtracks, most of the songs are very memorable and fit the areas they are in particularly well.
Combat: Skyward Sword. The enemies in SS are challenging enough, and you really need to think about the direction you slash with your sword, instead of just pressing a button as fast as you can to defeat an enemy. The shield is also more useful than ever before.
Characters: Skyward Sword. Every character has a unique personality in the game, and none of them feel bland, as opposed to other games in the series. The main characters, especially Zelda, Ghirahim, Impa and Groose were particularly great.
Items: Majora's Mask. With the many masks and the more traditional items, I think MM wins this category.
Bosses: Ocarina of Time. Most of the bosses offer a bit of a challenge, and they all require different strategies to defeat them. And they are pretty much all memorable too.
Exploration: Wind Waker. The sense of exploration was very exciting, at least to me, in WW. There are a lot of islands to explore, and you never know what you will encounter during your travels.
Overworld: Ocarina of Time The overworld in OOT was almost perfect. There are many areas, such as forest, mountains, lake, desert, and of course the field. All of them feel connected and aren't too far away from each other. There are many different villages, representing all the different tribes. The areas are all open for a bit of exploration too.
Dungeons: Ocarina of Time & Skyward Sword. OOT features many of the best dungeons in the series, such as the Forest Temple, the Shadow Temple and the Spirit Temple. But all of its dungeons were quite enjoying as they all had a diverse layout, some being more linear, others more opens, etc. With SS, each dungeon is really compact and has its own theme. The Sandship and the Sky Keep were particularly unique and fun to go through. Both of these games's dungeons feature good puzzles too.
Sidequests: Majora's Mask.
Puzzles: Ocarina of Time: Master Quest. I think this one has the most difficult puzzles in the entire series. Even the first dungeon is now challenging. I really scratched my head several times when going through the dungeons in MQ.
Sense of Epicness: Ocarina of Time. The story coupled with the cutscenes makes OOT the most epic Zelda game.
Method of Transport: Wind Waker. Navigating on the Great Sea on the boat with the excellent music and with enemies across your ways makes it my favorite method of transportation in the series. I also liked that you can use your items on the boat in different ways, such as the hook crane or the canon.
Sidekick: Twilight Princess. Midna is the best sidekick I think. She was helpful when needed, and was an interesting character.
Difficulty: A Link to the Past. ALttP has the most balanced difficulty of any Zelda game. Not too hard, not too easy, with a nice learning curve as you progress throughout the game.
Replay Value: Majora's Mask. MM has tons of things to do aside from the main quest, and even after several playthroughs, you can still discover many things (such as the scene with Anju and her mom). You can also refight all the bosses at any time thanks to the 3 day cycle.