Great essays, everyone! No, really, I've enjoyed reading this thread.
Um. This is more fiction in general, I guess, but these have always annoyed me.
One thing I hate is when the hero, after the villain is safely locked up, visits him and tells him exactly what he did wrong and how to fix it. 'Cause of course he'll never escape, right?
In Iron Man 2, for example, Creepy Russian Dude is in jail. Tony Stark visits him. And tells him how to fix the Arc Reactor he made. Like, really? You don't see anything wrong with that? Mr. Stark, I do not feel sorry for you after the beating you took before you managed to take him down the second time.
I also hate it when our heroes are running through the Mysterious Ruins chased by X monster, when they stop and wait to see if they've "lost it" yet, conveniently giving it time to catch up. I don't care if you need a break, we're being chased by a kraken. You can rest when we've made it outside and the temple/whatever's collapsed in on itself.