This is how I take notes in lectures:

• First listen to the lecturer
• Either when a fair amount of things have been said and you still haven't figured it out; or when you got the point already, then start writing things down. In the first case it is safest to copy down everything, while in the second case it is better to write it down your own way (presuming you have a book to check back later for details).
• Repeat the cycle.

Most of the time, I leave the lecture hall feeling like I get the general idea, which is helpful when I review the material later on. However, I think it really depends a lot on your writing speed: I write pretty fast, and stopping to take notes doesn't cause a problem. If I wrote only with half that speed, I'd probably use a different strategy.