Have you ever seen what happens when you take an average, non tech-savvy expert microsoft office user and then tell them that they have to use open office instead? they can't find anything! File formats can be an effective method of lock-in, but having a large base of users who are completely accustomed to using your product as the standard can be as well.

If OpenOffice were a perfect substitute for Office, and switching costs were zero, that would be it; the story would be over. Microsoft would only be able to give office away as everyone would be completely indifferent and simply switch to the cheaper product (in this case, OO, which is free). [proof by contradiction] Either they are not perfect substitutes or switching costs are non-trivial, or a mixture of both.

At the time I used straight LaTeX, but I made it work. The trick was to get a good editor and set up keyboard shortcuts for common things to blaze through the process quicker. Add on top of that a bunch of renaming functions in the preamble to save keystrokes for other common actions and keeping up isn't much of a problem.

That being said, I'm going to cast my vote for Lyx because you can still do all I suggested above, but it greatly aids in building tables, matrices, and other things that'll slow you down a bit. And don't be afraid to use shorthand that won't format properly when necessary, as long as you know what it says you can always fix it after class or during a lull in the lecture; I find this typically takes less than 5 min. And use lots of white space. And reconsider what the best way to keep notes is; when you have a medium with the flexibility of files, folders, etc, I find it's usually better to take notes by topic instead of chronology of when it is said.

Funny story, took notes all semester for my stat class that way and we got to use 1 page of notes for the final. About 20-30 minutes of copy/paste-ing gave me every equation we used, qualitative descriptions of what they do and when to use them, and a whole host of other useful stuff. Never studied beyond doing my homework (which I only did most of the time) but I got a 297 out of 300, highest grade in a class of ~150 and about half a standard deviation above the next highest score...