Good suggestions, there, thank you! Neon Genesis Evangelion and Cuckoo Song had already flitted through my mind, oddly enough - the latter particularly, since I used a somewhat similar device (use of a doppelganger's pov) in The Fetch of Mardy Watt, but without (I think) changing genre, and was wondering about the difference.

To add to your anime list, there are some very weird genre things going on in Hirugashi no Naku Koro Ni, though it's not so much as a once-and-for-all shift as a kind of compulsively repetitive series of whiplash switches.

DWJ is certainly a candidate: Hexwood especially, and perhaps Time of the Ghost? I'm sure there would be others, too, if I were to start working through them.