DOOM 3 - Anyone saying this game was a disappointment must not have understood that it was a sequel to a game called DOOM. I'd say that the game is too long for its own good, but it's a great shooter with amazing atmosphere.
Killzone - Comparing this game to Halo is like comparing Crash Bandicoot to Mario--yeah, they're in the same genre, but the games are totally different. Killzone is a pretty solid game with some technical problems, but isn't a bomb by any means.
Halo 2 - I think complaints about the game's single player are pretty silly. But maybe that's because I play Halo for multiplayer. And that's where I say Halo 2 fails--its multiplayer isn't as balanced and awesome as the original's. I still wouldn't call it a bomb.
Metal Gear Solid: The Twin Snakes - The game has some problems (new voice actors stink, old level design and new play mechanics make the game a tad easy, some cut scenes are ridiculous), but this is no way a bomb. The game plays well, and the addition of dog tags offers a great new challenge. Again, I don't understand the nominations of this.
With all that said, I knew which games would suck before they came out, so I wasn't super disappointed with anything. As for games that everyone else thought would be good but actually sucked, I offer: Grand Theft Auto: San Andreas, X-Men Legends, KOTOR 2, Mortal Kombat: Deception, Driv3r, Splinter Cell: Pandora Tomorrow, Ninja Gaiden.