Probably my favorite subgenre--I've seen all except Dead Zone (but I have seen eXistenZ, which has a dark twist). I don't remember if I've seen Dark City (I've seen several movies that sound similar, so I'll check it out).

The twist ending goes back to Greek tragedy. Oedipus Rex has one, but the audience would probably have known the story in advance. The real master of the twist is Euripides, whose plays pull the rug out from under the Athenians at the time (and he was quite popular in spite of doing so--except for Aristotle, who labeled such strategies as deus ex machina). The ending of Electra demolishes the pat solutions to the Orestes / Electra dilemma outlined by Aeschylus and Sophocles--and that's just one example of his subversiveness.

In modern films, Dead of Night (1945) has one of the earliest major twists (from the same year, The Strange Affair of Uncle Harry has a similar twist, foisted on the film by the prudish studio).

Polanski tends to feature a number of dark twists (and given what we know about his temperament, it's easy to speculate on why). The Tenant may be the most emblematic.

In my view, it's important to distinguish between the twists used to be subversive and those which are simply expedient or even amoral. The ending of Se7en (and all those Euripides tragedies) is subversive because it warns us to suspect our perspective on what is real since our perspective has been conditioned by the art that we've consumed; ditto for something like Unforgiven. The ending of Fallen is (in my view) simply amoral, put there for shock value. But that's just my perspective. (I'd be interested the perspective of Simon Dillon here.)