I usually refer to it simply as D&D, with referring to 1st and 2nd edition as AD&D. If what I'm talking about is more specific to edition then I'll be more specific.
3e as a general term - on rules posts I tend to be specific to 3.0 or 3.5 due to the differences (personally I only own the 3.5 rules so I try to make sure I only post on those threads).
Never have that problem. Probably because most of the folks I game with know about the various editions. Heck, I've got friends who don't know about Hero 5th edition yet as they turned away in disguist at the whole Fuzion thing and the New Millenium series.