I would make a directory structure like this, by topic, then by class:
Math
Math\MTH100\
Math\MTH101\
CompSci
CompSci\CSI101\
CompSci\CSI110\
CompSci\CSI120\
I would probably use a Wiki type note-taker too like Tiddlywiki at
TiddlyWiki
— a non-linear personal web notebook. It's free, and it can live on your flash drive, or on a free service called
Tiddlyhost. Tiddlyhost means you can access the Wiki from any browser, any computer.
Don't forget to back up all your files each week at least.