I didn't have much online coursework in my schooling until the very end. I had some computation heavy and writing heavy course work. I kept my notes in Word documents organized in folders by subject. This was great for history and some psych course, but in math and chemistry, note-taking/or transcription on my laptop was slow and cumbersome.
I now work in IT and have to take notes to keep up my skills.
Evernote is great for working on a project or research paper. I use to organize thoughts or to jot down random thoughts I may have on any subject. Using tags is crucial.
I use MS OneNote (http://office.microsoft.com/en-us/onenote/)to take notes on my various studies. Now, most of my coursework is online training books and modules and OneNote is the best. I tried Evernote, but it didn't work out. It is the most underrated MS product. It does screenshots (crop only what you want), resizes automatically with one click to your active window, built math equations and equation builder. This will be helpful for math, physics and engineering. They also have drawing which I can only hope will be awesome if you get a compatible tablet.
You can have it sync with your smartphone and use it online when your computer is not available. It also autosaves like Google Docs.