I have quite a few favorites. Pajama Sam, Putt Putt... But I must say my favorite was Spy Fox. It was fun, had great gameplay, good story and a good animation. I haven't played it for a while, but my favorite one was Operation Ozone.
Eh so many.
Nintendo 64: Donkey Kong, Super Mario Bros, Mega-Man +more sweet stuff
Nintendo DS Lite: Spider-Man, Spyro the Dragon
Play-Station 1: Spyro the Dragon, Mega-Man, Ultimate Snowboarding, some random car racing game +more sweet stuff