firebolt, I developed similar habits too and am working to banish them now! I often find myself saying "I'm sorry" in emails when there is really no need to do so--and sometimes I find myself using it in a kind of passive/aggressive way, where I'm really not in the least sorry but I'm using it to excuse the rude or otherwise crappy thing I'm going to say! You know, if I really feel I have to apologize for what I'm about to say, maybe it would be best for me to step back and review whether that thing needs to be said at all...
I worked briefly in the bakery at a grocery store, and quarters were tight w/a lot of traffic. I found myself constantly saying "sorry" to people as I crossed their path, moved over to get something, etc. The older man who was training me to bake said at one point "you know, you don't need to apologize all the time--you have as much right to be here and working as anyone else does!" I forgot about that until just now...guess he had a point, but it didn't really sink in at the time.