Super Metroid
Super Castlevania
God of War
Goldeneye

Lets keep it simple and keep them seperate, regardless if they are in a franchise. Franchises still have the one thats better than the rest so nominate what you think was the best one. Then you will have some franchises that have multiple games that deserve to be nominated. Madden, Fifa etc are the same game so the best one of them would suffice but the Mario's are different beasts that each one deserves consideration. Just my opinion.

The Simpsons

Legend of Zelda ocarina of time
Super Mario World
Super Metroid
Mario Kart
Waverace 64
Starfox
Goldeneye
Secret of Mana
Chrono Trigger
Act Raiser
Contra
R Type
Tetris
Ghouls N Ghosts
Castlevania
Metal Gear Solid
Final Fantasy 7
Tekken
Street Fighter 2
Ridge Racer
Mario 64
ISS
Rome Total war
Crysis
Call of Duty 4
Fallout
Fallout 3
Gears of War
God Of War
Resident Evil
Resident Evil 4
Pong
F Zero
Virtua Tennis
Thief 2
Halo
Shadowrun
Half Life
Home World
Ultima
Advance Wars
Punch out
Age of Empires
Command & Conquer
Gta 3
Gran Turismo
System Shock
Deus Ex
Zelda A link to the past
Super Mario Bros
Starcraft