What I like to do...
Well, I have diagnosed learning disabilities, so I have some academic accommodations through my university. Like, for instance, I'm *supposed* to have a notetaker, because it's hard for me to listen to my prof, read notes projected on PowerPoint, and copy all of this down at the same time!! So if a volunteer in the class can be found, I can get some notes so I don't have to completely freak out about missing information.
Anyways... I haven't always had that accomodation. Also, notetakers get sick too, since they're students like me.
So it's always good to have decent notetaking skills.
First...
1. Obtain lots of paper and lots of pretty coloured pens. Yes, more than one colour ink! Go nuts - as long as you can read it, it's good!!
2. Write the date/course code on the top. Also page numbers, esp. if it's looseleaf paper!
3. If the prof provides PowerPoint slides, especially before class, make sure you print those off and bring them along - this is so you don't have to rewrite everything that's put up on display!!
4. Write the title of the lecture at the top of the page (or the topic being discussed). Develop your own system of abbreviations for some words and develop a way of organizing info. Leave space for added notes afterwards!! (Don't cram it all onto one page!). Use indenting, bullets, arrows... anything that makes sense to you.
5. Any subsection "titles" write in another coloured ink. Important terms, dates, people - anything that the prof defines - write in another colour, or underline or box it off - anything so you know its important when you go back!
6. Put stars beside things that the prof seems to hint at or says is important - that generally means more likely testable on exams and stuff!!
7. If the prof mentions specific pages in a textbook, write those down beside whatever is discussed - in another colour ink from your regular notes! Its good to go back to.
8. If the prof mentions a project/essay/assignment in the future or deadlines - WRITE THOSE DOWN LIKE THIS and in another colour - and put it in your agenda/planner/PDA whatever. Organization is key.
9. Question marks are your friend. You don't understand something? Put a ? beside it. Or put your hand up and ask. If you ask a question, the prof stops rambling about stuff which means there's less stuff to write down.

Make sure you write down his answer though if the answer is important to your question (or if the question was important)
10. Profs are NOT there to be mean. Some are, yes. But use their office hours to ask them stuff. Most of them sit bored in their offices by themselves during their office hours because students are afraid of them... make friends with your profs, that helps you out a lot in the long run (for academic references, and better grades if you argue one!)
11. After the lecture, even if you hate it... take some time to review. Definitely within 24 hours of the lecture. THEN, add clarifications if you need to, to your original notes.
12. If you're like me, your handwriting can get pretty hazardous during class... so I type up my notes on my computer. This also helps if you want a "note buddy" in your class and they happen to miss one - then you can give them a nice typed copy of the class notes. They'll be grateful and you'll have help as you need it!!