I'm sorry dude, I don't think Ganondorf is that annoying. Maybe because I'm DARK MASTER, Ganondorf is just scared to mess with me =\? Also, there are so many bosses, it's hard to pick the most annoying.
Ganondorf is an annoying boss? personally i don't see it i haven't found any incarnation of Ganondorf to be annoying, however the second puppet he has you fight in Wind Waker is just ugh to me