It really depends on your learning style. Taking notes is great in that it keeps you engaged in and listening to the lecture while providing you with a reference to what your professor deemed important. But some people do just as well listening to recorded lectures or just studying from the book.
What I've come to do is fairly simple. I take notes on everything the professor lectures about (I started doing this as a note taker for my school's Disability Resource Center), and then after class I review the notes to ensure they are coherent (again, because I was providing my notes for others). Later, when I was studying I would read over parts of the book to confirm/add to the lecture material and note these things in the margins of the class notes. Then, when I was reviewing the material the next day, I would rewrite the notes, incorporating the lecture material, book material, and connections to earlier concepts.
It sounds like it takes a long time, but it really doesn't:
CLASS
-Review notes immediately after class: 15 minutes (tops)
-Look over book for more in-depth information: 30 minutes
-Rewrite notes: 45 minutes
CLASS
So in total, that's about an hour and a half. But it saves a ton of time later because you've reviewed the material as you've learned it and clarified it for later reference.
You should check out some other note taking methods, though. Just do a search on google and you should come up with a bunch to try out.
And remember - the best method for one person might not be the best for someone else. You have to figure out what works for you.