Xenogears

It's hard to choose between this and Super Metroid as my personal favorite game of all time, but I'm probably leaning towards choosing this game because of its length and for it being one of the few games to actually make me think...

Anyway, this is a perfect game from every angle. The music, the characters, the battles, pretty much anything that you could find flaws in any other game is perfect in this game. The main selling point, of course, is the multi-layered and very convoluted storyline. Though obviously very indebted to Evangelion, the 70 hours or so of story in this game is full of plot twists and shocking revelations about humanity, existence, God, love, death, and everything else in between. Not your typical RPG fare by any stretch of the imagination.

Also, don't listen to people who say disc 2 sucks... there is more than enough gameplay in this game that disc 2 comes as somewhat of a relief after 50 or so hours of disc 1's constant battles.

Just a perfect game... what more can I say?