I think one of the better plot twists I've seen in a video game would probably be in Metal Gear Solid 2. If you've beat the game, you'll know what I'm talking about. Freaking AIs, man.
I also liked the fairly obvious plot twist in Might and Magic: Messiah on the 360.
Ooh, ooh, and the big reveal in Operation Winback for the PS2! That was great.
Also in Shadow of Memories (Destiny in the USA) where you have to assemble all of the different endings to piece together the true one, and the MASSIVE plot twist it creates.
This is a weird one, but
I also liked the fairly obvious plot twist in Might and Magic: Messiah on the 360.
Ooh, ooh, and the big reveal in Operation Winback for the PS2! That was great.
Also in Shadow of Memories (Destiny in the USA) where you have to assemble all of the different endings to piece together the true one, and the MASSIVE plot twist it creates.
This is a weird one, but
In Tony Hawk's Underground, remember how that douchebag kid from your home town set himself up as the performer of all your sweetest moves, getting himself onto the pro skate team and completely screwing you over? Damn that one was great! excellent motivation for getting blistered fingers trying to top his score at the end.