I admit that I have a bad habit that I'm pretty sure would annoy some people: I talk out die rolls. That is to say when I roll the dice I always talk through it like this. "Ok, 20 shots needing a three to hit. Alright that's 12 hits. Now I need threes to wound. Ok, I got five wounds. You have a three plus save." So what's the problem with that you say? It's called communication, right? The problem is that I tend to talk through opponent's die rolls as well as my own.

I'm aware I tend to do it, and I try not to. But I still catch msyelf at it from time to time and I'm sure it annoys someone.
My own primary pet peave are:
-Touching my models. Depending on the army some of the stuff on my table is probably older than you are. Plus it's my property. Ask first. I have no issue with you admiring my work/the cool old models. But be polite and ask permission before grabbing one. I've been known to get pretty cross with some kiddie who just runs up and snatches something off my table.
-Trash talk/insults/name calling. If your opponent is a good friend and you talk to each like that all the time, then it's fine. (even if it's still annoying to bystanders) But why would you act that way with a stranger you are playing with in a casual pick up game or (god forbid) a tournement? This is not 4chan, so please be polite and respectful. Thankfully this is something that I have not experienced more than one or two times.
TR