I'm almost always messing with something, whether it's my eraser, a pencil, a yo-yo, some stress ball or anything that's close at hand. It's not really a nervous habit or a tic, I just end up picking things up and twisting them around in my hand or the like. My bedroom accumulates miscellaneous objects from me randomly picking things up and depositing them on the desk absentmindedly.
I remember I once spent almost an hour looking for a certain part from a Lego set only to discover later that I was holding the piece the entire time.
I tend to flinch easily... Very easily. Would that be a nervous habit? ;P
Nah. A nervous habit is something you do when you're nervous. If you flinch at things in general, that's just called being twitchy.