1. A single subject notebook – The trick here is that you stop using loose paper, or multiple subject notebooks entirely. You take notes for each class in it’s own single-subject notebook, so they’re always organized by lecture as well as subject. Finish a book? Start a second one. When you get to Finals Week, grab all the ones marked “Chem 102″ and don’t worry, coz none of your notes are missing.
2. The Cornell Notemaking PDF Generator – An awesome tool for those who use the Cornell method, with customizable options that make it easy for you to quickly create the type of paper you need before dashing off to class.
3. Evernote – If you’re the type to take notes on your laptop this tool is pretty awesome and a free alternative for those who like Microsoft’s OneNote. More importantly, they just created a tool to import data from Google Notebook, which got fired from “active development” earlier this month. Offers more features if you pay for monthly service, but the basic package gives you plenty.
4. Ubernote – Similar to #2, but doesn’t seem to have the character recognition feature. If you have no intention of using your iPhone camera or a Wacom tablet, then this is just as good as Evernote.
5. TiddlyWiki – Used Wikipedia? Same idea, smaller scope – so small you can save it to a USB thumb drive! Create a “Bio 187″ wiki for yourself, and then reap the rewards of super-portable notes!
6. WordPress – Just make a blog! You can use categories and tags to control the data, much like the Wiki suggestion, and be able to access it from any computer with internet access.

Admittedly, only a few of these tools are the old pen & paper type, but in this modern age it seems I see more kids in class on their laptops than with a notebook.