I use Evernote for note taking. Works really well. Available on Mac, Windows, iPhone, Android etc.
My basic strategy is to copy and paste the dot points and any key images/diagrams from the lecture slides prior to the lecture, and then basically just annotate and add to them as the lecture goes on.
If you want to fully get a grasp on the lecture, I find its easy just to make some of your own review questions that cover the key topics of the lecture. Then have a quick look over your notes and answer the questions in your own words. For me, explaining things in your own words is the best way to learn and retain information. If I just listen it's basically in one ear and out the other.
Then, come exam time, I go over all these and make some overarching subject review questions that essentially go section by section. I also might re-listen to some key lectures (provided they are recorded) and polish up my notes.
This can all get a bit laborious but since I've used this kind of method my results have been pretty solid and I tend to stay on top of things.
EDIT: Also, do people think it would be worth making a "General Jaffy advice/Q&A Thread" for stuff like this? i.e. personal strategies for study or general uni advice or getting around the campus etc.