1. "The villain was really the good guy." You've certainly seen these; a classic (read: public domain) tale retold from the POV of the villain, where we learn he or she wasn't really so bad after all. Marion Zimmer Bradley did it right in "Mists of Avalon" by not taking sides, and instead presenting both Arthur and Morgaine as good-hearted by flawed people doing what they thought was best. Most authors who run with the idea (and I include Gregory Maguire in this statement), though, simply hit the cast with a Spell of Alignement Reversal and pretend they're being creative. Plus, the whole "vampire's point of view" thing was played out about 5 minutes after Ann Rice cashed her first royalty check. Find a new idea, fantasy authors.
2. "Dark" superheroes. Yeah, I know, I'm not alone in this, but the news about Will Smith's next picture being about a superhero with clinical depression brought it to the forefront of my mind. Again, it's been done well, but by very few people, and a lot of the writiers mimicing the style completely miss the undercurrent of hope that exists in books like Watchmen and Dark Knight. Quoting Joe Rice quoting Grant Morrison, "Only a petulant teenager would mistake cynicism for realism."