Couldn't ever put them in order, but I'll elaborate a little:
Chrono Trigger-Best Jrpg I've ever played, more need dual/triple techs and time travel has never been implemented so excellently.
Rez-I've played it over 100 times. The perfect way to test your TV/sound system in the dark with 3 trance vibrators.
Shadow of the Colossus-Pacing, exploration, the colossi themselves are brilliant. One of the few examples of gameplay,story,mechanics, and setting working together for a central purpose.
Dark Souls-One of the examples I mentioned above. Every aspect plays into the isolation and indifference of the world. Fucking brilliant a midst the games released in the years before it.
Final Fantasy VI-This game and Chrono Trigger could by themselves be legitimate reasons to purchase an entire SNES.
Silent Hill 2-Atmospheric horror done right. Pacing, restraint and refusing to blow your load up front are lessons this taught and are largely ignored.
Okami-I was debating whether to put Zelda:LttP or OoT here, until I realized Okami did everything they did only much better with a beautiful art style.
Binding of Issac-Can't really explain it, makes the roguelike-style approachable and can rely too much on random-ness, but I've put way too many hours into it and it's brilliant.
Bayonetta-Everything I hoped DMC 4 would be, with so much more I didn't know I wanted. Kicks your ass in all the right ways.
Super Mario World-Nintendo was very smart in bundling this. Everything about SMB executed masterfully, with secrets that you had to truly work for. I wore out controllers with this game alone.