I took notes on my laptop extensively all through my undergraduate degree in Computer Science, and I always used OpenOffice.org Writer's equation editor. It has a nice, concise syntax, and it was, in fact, possible to enter even very complex mathematical expressions in real time, faster than my prof was able to write them on the board. This was true even for matrixes.
Here's an example of some of my notes made with OO.o: http://csus.cs.mcgill.ca/wiki/COMP-330_(Panangaden%2C_Fall_06)_Lectures
My linear algebra notes would be more impressive, because they often involved fairly large and complex matrix equations, but I never made those notes available online.
I had a colleague who also took notes in class who had quite a nice method - he wrote all of his notes in wiki markup, with latex for the mathematical expressions. He didn't have a laptop, but instead used a PDA and small, foldable keyboard.
An example of his notes are here: http://csus.cs.mcgill.ca/wiki/COMP-302_(Panangaden%2C_Pientka%2C_Winter_06)_Lectures
I think it's quite a nice result.
what's not to like?
No plugin that implements vi keybindings
But the more I use linux (Ubuntu in case you are interested), the more unhappy I am. It's the little things, like, keyboard not processing input on dual screen when there's no window open on that desktop. And configuring / changing (external) display configuration is simply broken. And high IO really brings system on the knees (even surfing is not possible while writing to a CD). Firefox is sloooooowwww. No exchange client. No out of the box AD integration. And so on and on and on.
Many of the complaints you list here I think are valid, because I'm using Ubuntu Linux as well and I have found myself thinking the exact same thing. Specifically, all of the trouble with X.org and dual-head, the high IO, and the slow firefox all resonate with me. None of these are enough to make me go back to Windows though; overall, Ubuntu offers a much better experience for me than Windows.
Mac OS, on the other hand, is very intriguing. Unix-based (FreeBSD, specifically), and yet has 110% hardware support. A thriving ecosystem of free software available (much [most?] of it ported from GNU/Linux). Overall, it seems like a pretty attractive target. There are just two things that really really prevent me from using it: the UI, and the culture. The UI I find to be bloated and ineffecient, and the culture feels quite closed. Until Apple opens up their OS and allows me to install it on non-Apple hardware, and stops bricking jailbroken iPhones, I just don't see Apple products as something I want to use. Better to target Ubuntu, which is technically very close, and properly philosophically aligned.
Oh, and as far as getting MS Office working on Ubuntu, apparently you can get it to work under Wine:
http://www.programmerfish.com/roffice-2007-in-linux/
I haven't tried it myself, though, so your mileage may vary.
"Protozoa are small, and bacteria are small, but viruses are smaller than the both put together."