Dark Cloud: Up there as contender for my favorite game of all time. Great music, fun and addicting gameplay, and incredibly unique. Legend of Zelda+Sim City is a combination you just can't go wrong with
Nier: The best soundtrack of any game ever, amazing story with tons of fantastic supplementary media adding to the characters and world, fantastic cast of characters, great new game plus content, one of the best and most daring endings in any video game, and just an all around gem. Can't praise this game enough.
Deadly Premonition: One of those weird games that's more soul over substance. The game mechanics aren't that good, but everything else excels. Great and memorable characters, intriguing story, lots of sidequests, and music ranging from bizarre to fantastic, yet always appropriate. One of those games that leaves a big hole in your heart when you complete it and move on.
Tales of Symphonia & Final Fantasy IX: Not much I can say about these that people haven't heard before, but I think both are the best in their respective legendary series. Full of fun characters, stories, and content, I can play these games forever.
Demon's Souls: This game makes a PS3 worth its purchase. Already cemented as a classic, it's not hard to see why. I believe it has the best music, levels, enemies, and atmosphere in its entire series. While the mechanics have been improved on by later iterations, it still holds up and is fun to play even now. In my opinion, it has the most Soul of the series with it's dark and gritty aesthetic and punishing gameplay surpassing that of its successors.
Honorable Mentions: Monster Rancher 2, Metroid Prime/Super Metroid, Shadow Hearts 2, Shin Megami Tensei II, God Hand, Zero Escape Series, and Kagero III.
