I say..
1. Legend of Zelda: Ocarina of Time (N64) I love my other top 4 favorites but they don't come close to OOT.
2. Chrono Trigger (SNES) The only RPG I've really, really liked. Great story, gameplay, music.
3. Pikmin (GC) Very close to Chrono in my top 5. A very different game but very well done.
4. Legend of Zelda: Majora's Mask (N64) Lots of sidequests, very good game.
5. Super Mario Bros 3 (NES) One of my favorites, took the first SMB and added lots of great additions -- powerups, worlds, music, story, etc.