I'll put my guesses under spoiler tags. Purely for bragging rights, others should post their guesses before looking at anyone else's.

(SPOILER)

These I'm pretty confident about being on the list:

FFVI
FFT
Suikoden II
Chrono Trigger
Xenogears

These I think are pretty likely:

MGS 3
Zelda: Link to the Past (bumped this one up in confidence after WK's last post)

These I'm guessing only because I'd be surprised they're not somewhere in the top 100 otherwise given what I've read from WK and elsewhere:

Persona 3
SMT: Nocturne
Some Guilty Gear game given your love of fighters (a more random guess after racking my brain, because I wanted to include 10 and this would be a third non-RPG). I do not know the series at all so can't pick one, or maybe this is where you cheat and pick the series as a whole.

I'm also surprised Suikoden I is nowhere in the top 100, but I don't think it's in the top 10.

Other fan favorites that I'm willing to call as NOT going to be there: Ocarina of Time, FFVII.