Seeing as how Hardcore Gamer said he wanted to spread this to the other consoles, I decided I'd just do it for him (because it's 2:44 A.M. and I can't sleep).
This is simple: Just give us some games you think should make the Top 100.
I'll start out with some of my favorites:
Castlevania 4
Chrono Trigger
Claymates
Contra III: The Alien Wars
Donkey Kong Country
Donkey Kong Country 2
Doom
Earthbound
Earthworm Jim
Final Fantasy 2
Final Fantasy 3
F-Zero
Kirby's Dream Course (the game that made golfing fun!)
Kirby's Dream Land 3
Mortal Kombat
Mortal Kombat 2
Mortal Kombat 3 (I love this game because of that weird tournament type thing, where, after you beat it, you can see a bunch of fatalities)
Ninja Gaiden Trilogy (The first three all in one game??? Blasphemy!!!)
Secret of Mana
Street Fighter 2: Turbo
Super Mario Allstars + Super Mario World
Super Mario Kart
Super Metroid
Yoshi's Island
Zelda: A Link to the Past
Zombies Ate My Neighbors