I find it depends on a) Your familiarity with the subject and b) How fast/technical the lecture is.

If for instance I'm seeing the topic for the first time and the lecture isn't going at a breakneck pace, I'll take notes for the "Abe Lincoln effect" that J.Polak describes (apparently Lincoln even read his newspaper aloud to make sure the day's news stuck in his head).

If I've seen the topic before I'll generally take notes, but only sparse notes on particular parts of the lecture I think are interesting.

One way around all of this that I've seen is taking pictures of the blackboard. There is one professor at uga who brings a camera with the flash turned off and the shutter set to silent who asks the speaker before the lecture if he can take pictures so he can avoid getting lost in his notes.