I came across this Managing Collegiate Paperwork article and thought I'd pass it along with some of my own thoughts.
I love the idea of the CollegeCase. Heck, I wish they had something like this for projects I lead in the "real world". They do have one for taxes, but then I have a wife for that. I do think $25 is kind of a lot of money, but you are getting a bunch of good checklists and overviews of what needs to be done. They also have one for college applications which I may get for some of our seniors in HS, it looked great.
As for myself, when I was in school I had a big 1 1/2 or 2 inch ring binder which held lined paper with my notes and all handouts in the pockets. This worked great for me, though now everything is filed on my computer or in my GTD list.
Which brings me to the last point. I read Getting Things Done a bit over a month ago. So far I'm still using it, but struggle when time gets busy. My list is so ridiculously long and sometimes feels overwhelming, but it has gotten me to really follow through with things I have put off, and it's increased my confidence level enormously.
I actually use the GTD ideas with RememberTheMilk (sometime soon I'll post exactly how I've set this up). I can't express how useful this has been.
So, there are my college organization thoughts, as stolen from other people.