I personally have problems with the 4 subject. The idea is good and sound, and I do like them for some things but I think there are problems. Many lectures seem to offer a slide print out - one of these for each lecture will quickly make your 4 subject document areas too thick. There aren't heaps of pages in each section, and if you fill one up you have to start carrying around additional books. If you lose your 4 subject (i'm a losing things person, if you're not then maybe its ok) then everything is gone for every subject. You can easily leave it at home and then everything is out of whack.
I have a ring binder which I leave at home all the time. One of those large ones. To school I bring a ruled a4 pad with holes down the side. I take notes on this. I also bring one clear sleave and a paper clip, I put handouts etc in here. When I get home I remove the notes, put the in the correct part of the folder, and do the same with print outs. That way I have everything in one place.
If I take my little laptop then I print out my notes.
When doing essays I like to print out journal articles. Maybe not environmentally friendly but I get so much more from it if its right there, high lighted, noted etc. When I am finished with my printed out journal I also put that in my ring folder, along with the draft versions of my essay. It keeps everything all in one thing.
Once the semester is over you write the details on the binder, and store it away with your text books for whenever you need to remember what you learnt.
The upside of this system is:
Not much to carry everyday
If you lose what ever you have on any given day, you have only lost one day of notes
It keeps absolutely everything all together
Filing stuff away gives you a chance to read over your days notes
If its too hassely to do everyday make an "inbox" on your desk for once a week
If you borrow paper, get excess print-outs - whatever - then you can still put it all in
Its up to you. While its not really that "important" what system you use, make sure you find one that works for you. Nothing is worse than when you know you had a page of notes and it can't be found, and you need it.