Mine is definitely the mobs spawning in my house, as well. Stellardawn, while I appreciate the fix suggestions, I would really rather be able to put my bed up against a wall if I'd like to. I prefer to put my bed in a corner of my house because I think it looks nicer that way, and because there it's not jutting into my house and taking up a large amount of space. I just really don't like that despite the fact I have four walls around my house that somehow a skeleton can teleport inside magically and start shooting me.
Not sure if this counts as a glitch, and they might have fixed this (haven't played as much lately as I used to), but a close second is Endermen picking up player-placed blocks. I have expansive building projects that would be a super-pain to try to make three or four-blocks thick, and I keep seeing "Enderholes" appearing in them... It's just annoying. I spent days, probably weeks, on that project, and I don't want to be running around replacing blocks to keep my projects from looking like swiss cheese.
Just so I don't sound like a complete negative nellie, though, I kind of like some of the lighting glitches. I always kind of chuckled when my chest would somehow mysteriously be dark. I also thought it was amusing whenever I'd come across a water block that wouldn't be flowing down into a cave it was next to, but just sitting still in mid-air. :3