I could come up with a very long list, most probably romance related, but at the same time I don't think there's any such thing as a specific plot device thats bad. Simply put, its only bad because of the way it gets used by uncreative writers. Heck, even the Mary Sue doesn't have to be a bad thing. Kamina from Gurren Lagann was essentially a Mary Sue and I don't think anyone who watched the series is going to criticize him for it.
As an example, these days I tend to cringe everytime I hear the word "amnesia" involved in a plot (usually video game plots) However, I have no doubt that amnesia COULD have some interesting plot-related uses aside from a convenient excuse for the hero to not know something at a critical moment or to remember something at a critical moment. I'd never play the game myself, because I'm not too fond of WRPG's, but Planescape: Torment is often praised for its story and makes interesting use of amnesia as well.
Knights in the Nightmare is another one, the plot of which I found to be surprisingly interesting. You're basically a disembodied spirit trying to get back to your body after you were killed before the start of the game. You don't remember a thing, though, and spend the game following that singleminded goal while slowly piecing together what happened.