Ok, let's see.
Bravely Default: It has one of the best plot twists because it doesn't have a dramatic plot twist reveal. It gives you hint after hint as to who the bad guy is, but leaves it up to you to draw the conclusion. It's a fantastic twist when you uncover it, as is the actual major reveal it does. But it really feels as though the game is saying "if you haven't gotten it by now, too bad", rather than actually trying to psyche you out with a plot twist.
Super Metroid: The baby Metroid's final appearance. You spend the entire game questing after this thing. You get into the final corridor, and you see foes that are powerful, taking several Super Missiles to take down. Then the "baby" swoops in and reduces one to dust in seconds. It then chows down on you... Only to see you as it's mama. It's such a fantastic little twist, and it culminates with one of the most heart wrenching scenes in gaming, when the little baby is so concerned with saving you that it perishes at the hands of Mother Brain. AND THEN YOU CALL DOWN THE THUNDER.
Mark of the Ninja: Ora's identity. Foreshadowed the entire game, perfectly sensible, yet it's executed so well that very few people actually clue into it before beating it.
Robotech: Battlecry: My gosh, this game does not get enough love. The twist in this case is Skarrde's defection. Another one that was well set up, even if it wasn't exactly a huge moment in the overall plot.