My top PS3 games that aren't in every "best PS3 games" list are Yakuza 3, Demon's Souls, Valkyria Chronicles, and if you're into PSN games, Flower.
From the main pick, yeah the Uncharted series is the best thing on PS3 and needs to be owned by every PS3 gamer. God of War 3's the game that gets the most out of the box, Killzone 2's best for online, and inFamous is a tremendously fun open-world game.