I'm a bit old school and prefer taking live notes with a pencil and note pad. If it's important, go back and turn these into a more readable document.
As professor, I find it HIGHLY distracting when students are pecking away at their laptops instead of actively participating in lecture...which is hard to do when part of your attention is devoted to formatting Latex equations. Moreover, for anything that involves a plot or a graphic...learn to sketch it in your notebook. You'll be amazed at how much better you will comprehend the material.
That stated, for my RESEARCH (in condensed matter physics), I keep a series of Latex and Mathematica notebooks organized by topic, date, and student involved on the project. The Emacs ORG mode looks interesting, I'll have to check it out.
I have been doing things this way for almost 25 yrs and I require my PhD students to do the same. I have common group DropBox & each of my PhD students has a folder within the Group folder. Also, each final paper has a separate directory with either all input files or original version of the computer programs that were used for that paper.