Flies. Their physical appearance may not bother me (although their eyes are pretty creepy from up close), but the sound that they make is annoying when I'm in fairly loud public spaces but absolutely terrifying when I'm alone in my room in near-absolute silence. Far too many times, I've been asleep in my bed and then I've been woken up by a fly buzzing in my room and I've ran to the bathroom (the room opposite my bedroom), refusing to come out until my mum kills the fly (yes, really).
In case you haven't figured it out yet, I have a phobia of flies.