I think I can classify bad endings into three types, at least in my view of things -
--"Classic" Bad endings, IE endings that obviously indicate to the player - YOU FUCKED UP! The severity of the fuck up may vary from 'being cannibalized' to 'turned into a doll and used as a plaything by a loli' to 'You don't get to stick your dick in her.' depending on the game.
--"Possible" Bad endings, IE endings that very well could simply end a route on it's own (and may in fact be indicated as such that they aren't really bad ends), though they aren't one of the primary route endings.
--"Actual End" Bad endings, IE endings that wrap up a storyline and are considered better than a bad ending but really aren't.
Now, examples as to all
As to the first, I have to look at GnK, specifically the Makina bad end.
To the second, I have to give this one to Mind of Steel end from Fate/Stay Night. It's a rather simple bad end that may not in fact be a bad end in another route. It could easily have been one of it's route endings (And indeed some in the fanbase would prefer it over the True end.) Another excellent example of this is from F/SN as well, the Sparks Linear High end.
When it comes to the third, the one that initially jumps to my mind is Ahika's Normal Ending from Tsukihime