Unfortunately I can't find any of the Zelda games or SSBM anywhere, so my list consists of:
Goldeneye: Rogue Agent
Bloody Roar: Primal Fury (used to play this in the arcade more than Soul Calibur)
And I guess Pokemon XD: Gale of Darkness
SSBM is still heaps of fun when I occasionally play it at lans, though I'm actually quite good (imo) at SSB on N64.
And btw Lylat Wars (or Starfox 64, what most of you call it) was such an awesome game, but I got bored real quick from Starfox Adventures.