The 90s is full of 'Games of the Decade', I mean look at the list. Most of these would win Game of the Decade in any other decade. However, only one can be chosen and it would be a god among gods. Or I should say 'goddess', when the best of these, and my favourite game of all-time, is The Legend of Zelda: Ocarina of Time, my vote.
Of this list I'd say; Ocarina of Time > Super Mario 64 > A Link to the Past > Super Metroid > Age of Empires II > Doom > Super Mario World > Sonic 2. I haven't played Final Fantasy VII and Chrono Trigger, so I can't rank them myself, but recognise their greatness. Of the 90s as a whole though, my top 10 would be; Ocarina of Time > Super Mario 64 > Yoshi's Island > Link's Awakening > Anno 1602 > Mario Kart 64 > Theme Hospital > MediEvil > Kula World > Star Fox 64 > SimCity 3000 > Asterix > GoldenEye 007 > A Link to the Past > SoulCalibur. Okay that was 15 actually but, yeah, the 90s.