Duh! Flandre's theme is overpopularized but with good reason. It's catchy and there are thousands of remixes of it, heck, you could consider UN Owen its own genre, aside rock, classical, techno, dubstep, what have you...
I also love Septette for the Dead Princess, Bad Apple, Broken Moon, Lullaby of Deserted Hell, and Beloved Tomboyish Girl.