I grew up with the SNES, so I little, if any, experience with the genesis. Here's my SNES favourite list:
Illusion of Gaia
Donkey Kong Country 1-3
Super Mario RPG: Legend of the Seven Stars
Chrono Trigger
Contra 3: The Alien Wars
The SNES was such a great system. It may have had it's share of crap, but there were a lot of great games.