I will not say that I am the absolute guru in these two aspects, but I’d like to offer some tips that have helped me. Pick and choose; they may help you, too. For any of this to work, though, you’ve got to go to class! I can’t stress enough how important it is!
So let’s start off with taking better notes.
You can do this manually (with a notebook and pen/pencil) or digitally (with your laptop). I prefer the latter because I can type a lot faster than I can write; also, my handwriting tends to get very sloppy when I’m tired or cranky.
But, if you like to do it old-school style with your best notebook and writing utensil, there are a few ways to take more and better-organized notes:

1. Use abbreviations!

Instead of writing numbers out, write 1 or 2 or 5826. You’ll save time.
Instead of writing out the word “and” all the time, try writing a simple ”&“.
Instead of writing out the word “or”, try a simple “o”. It’s Spanish!
For “with” and “without”, go with “w/” and “w/o”.

2. Eliminate useless letters!

This works when taking notes, too, I promise. Don’t mix your letters up, but try to elmnte vwls.
You could also substitute “g” for “ing”. “Studying” becomes “studyg”.

3. Test drive the Cornell note-taking method:

Divide your notebook page into sections. Take notes on the right. Leave the left blank until after the lecture (where you’ll write keywords). And then save the bottom section for a few sentences summarizing the lecture’s “point”.

4. Pay attention and write down the right stuff!

Again, WikiHow is a great resource:

Watch for signal words. Your instructor is not going to send up a rocket when she states an important new idea or gives an example, but she will use signals to telegraph what she is doing. Every good speaker does it, and you should expect to receive these signals. For example, she may introduce an example with “for example” as done here. Other common signals:

So that’s all great. But what if you’re looking for some software to help you out?

1. Don’t study in your room. Don’t study in your apartment. Don’t study at “home”.

Choose a place that’s neutral and doesn’t have previous associations. You’ll be less distracted this way. Go to a library (haha, shocking!). Try an empty classroom. Go into a basement somewhere. Go on a roof, whatever. Just choose your spot and stick with it. Associate that spot just with studying. You’ll get a lot more done with fewer distractions.

2. Bring a music cd or two or three.

I’ve heard about this before, and so I’ve tried it out. It works for me. Bring your favorite music cd of the moment. Set it up to play at a low volume. Hit “play” and get to work. While the music plays, only get up to go to the bathroom. Otherwise, stick to the books. Once the cd finishes, take a good 5-15 minute break. Put in a different cd. Do it all over again.
With good, straight 1-hour intervals, you’ll get a lot done, and time will fly by. And you’ll feel so accomplished, knowing that you spent a good 3-5 hours studying.

3. Keep your pen/pencil moving.

When I study, I typically print everything out, in order to have tangible notes. I’ll highlight. I’ll circle. I’ll box. I’ll underline. The key thing here is to stay focused, stay concentrated. When I was preparing for the finals, their advice to stay on task was to constantly move your pencil, constantly keep a rhythm. Stay in the material. Tap your pencil. Swing it back and forth through your fingers. If you have a hard time staying attentive on the material, try this method.