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the wiki is a good idea
There’s another wiki program at Tiddlyspot that will allow you to access it from both the client and the server side - so you can download the online wiki to a flashdrive, run it off of any computer, save the changes and upload it later to the web. It’s free. That might help with the class notes.
But for the other — is it possible to just use a laptop at school? Then you have all the programs you need with you during the day, and you can still upload the info to the school’s computers when necessary. You can make what ever changes you need to your host documents, and FTP from home. I second the idea of your own space: if nothing else, it’s dedicated, and won’t change if you ever switch to a new school.
And although I love my mac, if getting a laptop is an option, maybe try a tablet computer. They have handwriting recognition, and there’s the OneNote software that’s supposed to be pretty good.
I’m a student, and I use Word docs and the wiki all the time. I tend to save the pdf until I know I’m switching from the mac to the pc or if I have to upload it. I also use Math Type, but in a pinch, you can use the old-school math notation using the regular keyboard symbols that appear in Word — these can be cut+pasted into the wiki directly.
The great thing about the wiki is that it permits tagging: so if you’re talking about say, differentiation on one day, and power series later on, you can tag them to each other and explicitly put the connection there.