Ill have to agree on Final Fantasy XIII, hands down that is one of the most underated games of all time. Perfect story, perfect battle system, perfect world design, the game was a breath of fresh air into the franchise, and its the first Final Fantasy where i liked all of the characters for once. And im glad many people have mentioned it so far because im sick of all the haters / reviewers comparing it to older games in the franchise. Just because they dropped the make-up wearing antagonist, changed the old and dried up battle system and streamlined the game doesnt make it bad.
Another game is NiGHT's into Dreams. One of the most fun and innovative games i have ever played, when you fly in that game you feel like a bird, as long as you have the original Sega Saturn and 3D controller that is =P.
Another is Metal Gear Solid 3, it was rated the lowest out of the series but i honestly think it is the best alongside Metal Gear Solid 1. The story wasn't overblown, it was a much simpler game than the others which in my opinion is better. And you have got to love the environments, Snake belongs in the jungle. And the bosses were badass too.
Another is Sonic Adventure. Hands down the best 3D Sonic game. I loved the free roam elements, the music was absolutely amazing, the graphics were flashy, the bosses were fun yet challenging, the action levels were fast and fun, amazing level design and world design too. And Perfect Chaos, what a BADASS. What more could you want from a Sonic game?