The most effective way is to take notes on a pad or a spiral notebook. Eventually, run them through a scanner.
(How are you going to enter equations, draw arrows and diagrams, etc., with a keyboard? If you have a stylus "works almost as good as a pen!", just use a pen on paper. Yes, I'm old, and I wear a watch, too.)
This is a fascinating challenge. I feel like it's probably possible to enter and edit equations as easily with the keyboard as with a pen; certainly you can do so for numerical expressions, using RPN.
I wrote a quick hack at http://canonical.org/~kragen/sw/dev3/rpn-edit#3_1_7_1_15_1_1... that almost does a reasonable job; I think that, although it doesn't quite reach being a usable equation editor, among other things because it doesn't have "=", it shows that one is possible.)
I wrote another related quick hack at http://canonical.org/~kragen/sw/81hacks/autodiffgraph/ with a slightly different take on the problem, where the objects you calculate with are continuous functions of x rather than pure numbers.
I defy anyone to reproduce a chalkboard full of eqvations, diagrams, arrows, etc., with a laptop and keep up with the professor.
Besides, my spiral notebook's battery never gives out, it's light, it's $.79, nobody is going to steal it, it doesn't make any noise, it doesn't distract anyone behind me, it won't break when I drop it, etc. Besides, no notes are complete unless you have a coffee cup ring on it.
You raise some good points, and many of them are related to why I take most of my own notes on paper. However, laptops far excel spiral notebooks at their ability to produce coffee rings on your notes; with the latest algorithms, you can produce many such rings per second!
That only works if you can 1) write fast and 2) decipher what you wrote earlier. I'm fortunate enough to be able to meet both of of those characteristics, but I know one of my colleagues specifically learned LaTeX and emacs so that he could take notes quickly in math classes. LaTeX for equations, emacs drawing mode for ASCII art diagrams.
My first semester in college I discovered that I could not read my notes. With some effort, I fixed that.
40 years later, I can still read the notes, but I no longer understand them because they have no context (the professor's words). At the time the notes served to remind me of the lectures, but not anymore. I wish I had made audio recordings, but the idea never occurred to me, nor to anyone else.
The notes, no. The lectures themselves. For example, one of them was a Feynman guest lecture on potato chip worlds, which I'm sure if it was recorded it would be a classic today.
(How are you going to enter equations, draw arrows and diagrams, etc., with a keyboard? If you have a stylus "works almost as good as a pen!", just use a pen on paper. Yes, I'm old, and I wear a watch, too.)