OoT has to be my favorite Zelda, it plays exactly like a 3D version of ALttTP with the best elements of Link's Awakening thrown in for good measure, and then on top added Epona which was pretty revolutionary. There were 8 main dungeons, and three or four smaller dungeons with plenty of variety. The game had no real glaring flaws about it. I know this game backwards and can complete it with zero deaths and all the items since I have replayed it about 6 times. The only thing I have never done in the game is catch the fabled Hylian Loach. Caught the 20lb fish, but not the Loach, since I have never seen it. Best pic I've seen is here:
Majora's Mask for me played completely different. The entire Clock Town was a work of genius, with characters going off at specific times like clockwork. The graphics and sound are much richer than in OoT, and the story was much more important and is much more tied in with characters in the game. Being able to use four characters was just awesome. The dungeons were tougher than the one in OoT. It was great to see so many characters from the original OoT to return. The game had some glaring flaws though that pretty much ruined it. The sidequests took over the actual game, so there were hardly any dungeons. You lost a lot of items and rupees when you went back in time and all the dungeons reset back and you have to do everything again. For me, this made me go into "race mode" just so I didn't have to redo things tons of times, and caused the game to be over before it begun, which was a shame. You also had to wait a long time for the time-based events to start even when using the song of double time (annoying on the real N64 when there is no way to speed the game up), and if you messed up you have to warp to Day One and repeat everything. This game was still great because there are elements to it which I wish could have been in OoT.
Wind Waker was a mixture of Majora's and OoT, but added new stuff. The combat was flat out better. The story was okay. I thought the graphics were sharp and great to see in motion. Garrickson looked a lot like Freddie Mercury which is a always a plus. It all fell apart when you had to collect all the triforce charts/pieces etc. when you were in the sea for hours on end, and these annoying Peahat enemies prolong it by knocking you off the boat. You had to change the wind direction when you want to go somewhere else. Gannondorf looked totally wrong, like a Bishop chess piece. The dungeons were also a bit too easy. Overall it was still pretty good though.
The GC as a whole has been a little disappointing since it has become more of a mainstream thing rather than just for hardcore gamers like N64, but there are a few classics in there that made my GC purchase worthwhile many times over.

Majora's Mask for me played completely different. The entire Clock Town was a work of genius, with characters going off at specific times like clockwork. The graphics and sound are much richer than in OoT, and the story was much more important and is much more tied in with characters in the game. Being able to use four characters was just awesome. The dungeons were tougher than the one in OoT. It was great to see so many characters from the original OoT to return. The game had some glaring flaws though that pretty much ruined it. The sidequests took over the actual game, so there were hardly any dungeons. You lost a lot of items and rupees when you went back in time and all the dungeons reset back and you have to do everything again. For me, this made me go into "race mode" just so I didn't have to redo things tons of times, and caused the game to be over before it begun, which was a shame. You also had to wait a long time for the time-based events to start even when using the song of double time (annoying on the real N64 when there is no way to speed the game up), and if you messed up you have to warp to Day One and repeat everything. This game was still great because there are elements to it which I wish could have been in OoT.
Wind Waker was a mixture of Majora's and OoT, but added new stuff. The combat was flat out better. The story was okay. I thought the graphics were sharp and great to see in motion. Garrickson looked a lot like Freddie Mercury which is a always a plus. It all fell apart when you had to collect all the triforce charts/pieces etc. when you were in the sea for hours on end, and these annoying Peahat enemies prolong it by knocking you off the boat. You had to change the wind direction when you want to go somewhere else. Gannondorf looked totally wrong, like a Bishop chess piece. The dungeons were also a bit too easy. Overall it was still pretty good though.
The GC as a whole has been a little disappointing since it has become more of a mainstream thing rather than just for hardcore gamers like N64, but there are a few classics in there that made my GC purchase worthwhile many times over.