Oh wow... hmm... So hard to choose just a couple of them really...
I'll do my best for a top 7.
7. Sonic Spinball
6. Super Smash Bros (Again, if you consider the N64 era to be old school now)
5. Super Mario Bros 3
4. Mario Paint
3. Sim City (SNES baby!)
2. Final Fantasy 8 (if you can consider that old school, if not, just remove this from the list)
1. Super Mario RPG
And for another couple of favorites if FF8 and SSB aren't old school - Legend of Zelda: LttP, Chrono Trigger, and Worms: Armageddon