I'd like to add 'hover the mouse in the magic spot' to the list, where UI elements are hidden until the mouse is above them. Facebook and Google are primary offenders. It's so goddamn hipster and entirely useless, even harmful.
I like using keyboard-only interfaces for browsing (currently through Firefox's Pentadactyl plugin). Jira has some things that are hidden until hovered over, and it completely breaks the keyboard-only interface.