Ubel Blatt
Spoiler (mouse over to view)
Instead of Koinzell being the saviour and all that, he turns out to be the opposite. Also, the lances of betrayal being the true heroes.
One Piece
Spoiler (mouse over to view)
Ace dying and showing a darker side to the otherwise comedic series.
Aphorism
Spoiler (mouse over to view)
Innocent looking school turns out to be a bloodbath.
Usotsuki Mi-kun to Kowareta Ma-chan Totteoki no Uso
Spoiler (mouse over to view)
Mii-kun not being Mii-kun.
Full Metal Alchemist
Spoiler (mouse over to view)
Selim is Pride.
There's probably much more but I can't recall them now.
Thanks!