Perhaps the most famous of DC's clever twist endings is that of the ending of The Long Halloween - and deservedly so, as it gets its rep for being a simply fantastic story.
The Long Halloween is largely a mystery story, centered around a mysterious serial killer named Holiday. Half-way through the story, it appears as though this mystery is solved, when Holiday is revealed to be Alberto Falcone, who has been systematically killing off people on holidays in order to spite his father for never letting him join in the mafia activities of the Falcone families.
At the very end of the last issue, however, things suddenly take a drastic change. Gilda Dent - Two-Face's partner - is revealed to have been responsible for the majority of the Holiday murders, in an attempt to get vengeance for her supervillain former paramour.