Vagrant Story. I actually was playing it once when it first came out, and had the rather startling realization that it didn't actually have voice acting. Somewhere along the way I could just hear all the characters acting out those speach bubbles to the point I kinda forgot I was reading them. How many games can that be said of? That the the story sucked you in so much you forgot you were playing a game?
Koudelka. Great game, but would be so much better with new graphics and a new battle system. One like Shadow Hearts 1, and not as complicated as SH2 or 3.
Return of Samus, Link's Awakening, Silent Hill, Blaster Master, Soul Blazer, Tenchu, Turok one or two (the only good ones/ones without terrible glitches)
And an actual sequel to Primal/Skies of Arcadia or Rogue Galaxy