Gotta think about it. The top 3 are easy though.
Chrono Cross:
(SPOILER)Lynx switches bodies with Serge. Not only does he "steal" all of your party members, but he uses them to kick your ass, and brutally stabs your love interest too. Did I mention that you'll be playing around 60% of the game in Lynx's body? No one saw that coming.
Fire Emblem 4:
(SPOILER)Your entire party(including the main character) is killed halfway in the game, by your brother in law. Did I mention that he's now married to your amnesia stricken missing wife? She's pregnant with his child too. The second half of the game picks up years later. You play as the main character's son, and the main villain is your half brother/cousin.
Baten Kaitos:
(SPOILER)The traitor in your party(who has been helping the enemy the entire time) is none other than the main character Kalas.
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