The one that stands out to me right now is the main (or one of the mains) character having amnesia. So many RPGs I've played have done this. Final Fantasy V, VI, VII, Breath of Fire IV (if I'm remembering right), and Xenogears. I initially groaned when Xenogears did it, but everything at least added up in a clever way.

If I run into one more RPG protagonist suffering from amnesia I'm liable to break the cartridge/disc (not really, but you get the idea).