These aren't in order:

1. Project Justice
2. Breath of Fire 4
3. Star Ocean 2
4. Final Fantasy Tactics
5. Streets of Rage 3
6. Final Fight 3
7. Mega Man X
8. Three Wonders
9. Bomberman 64
10. Mario Kart 64

Honorable Mentions:

Fire Emblem: Seisen no Keifu (I think this is Fire Emblem 6 or 7, I don't remember)
Ogre Battle
Lunar Legend
Demon's Crest
Castlevania: SOTN
Super Mario 64
Mario Tennis
Final Fantasy 4, 6