I'm just starting med school, and so I'm answering your question based on my non-med school classes. I have a wacom USB tablet that I would take to lectures and draw any figures with. I'm avoiding tablet PCs for now because I consider them underpowered and relatively frail (and not exactly cheap). I'm putting off getting a Tablet until I start seeing patients for several hours per day.
Anyway, before class, I would copy or type the text into MS OneNote and insert any figures / slides. During lecture, I would type and copy / paste any comments / clarifications, type in potential test questions, and mark it up during class. I made sure that any figures / penart were in their own tab if at all possible so they don't move around which would mess up the alignment of call-outs during the cleanup stage. I would finalize my notes after class and e-mail a PDF to the prof for a disabled student, friends who missed class, etc. I like having everything on the laptop because I got tired of making hardcopies of everything. Plus, you can search for stuff instantly. If you use a laptop like this you must religiously back up your machine every day with a reliable program like MS Live OneCare (be sure and test the program (whatever you decide to get) by deleting a file or trying to restore onto another computer) because the machine will fail and you could lose everything. Most backup programs don't really work well in my opinion.
I'm not sure how I will refine this strategy for med school. I have gotten good use out of MindManager for my research and I might start using it to develop my own little practice tests during lectures because you can insert figures, labels and show/hide/mark stuff quickly and easily. Anyway, hope that helps.