This is a rather tough one; it comes down to Ocarina of Time, Castlevania: Legacy of Darkness, and Super Smash Brothers. I'm probably going to say Castlevania; it managed to have both the adventure style feel of LoI and such (the villa), combined with platform style stages without dedicating entirally to one. The magical nitro was still irritating, however if I recall it was much simpler than in the original Castlevania 64; also the difficulty felt "just right" in my opinion for the jumping. I did die a lot in that regard, but the frequency of checkpoints made it more annoying motivation, than a major setback; it's rather rare for me to laugh at my own deaths but I did a couple times in the tower of executions. It also fixed my major complaint with the previous Castlevania 64, which was the difficulty of getting the better endings.
either Banjo-Tooie, LoZ Majoras Mask, and SSB... Well, I'm going to say B-T, because one you play SSBM, you can't go back to SSB, and Majoras mask was close second. (B-T and LoZ:MM survived the test of time).