Oh my goodness. Evernote is so wonderful for school; I cannot even begin to describe how much it has helped me. I am naturally a data hoarder, unabashed in my inability to actually maintain it all, but so addicted to the idea that nothing can be spared. That sort of behavior simply isn't conducive to a good academic experience.
A Trap for Every Keeper
I know a lot of people use Evernote for every aspect of their life, and prefer to keep a minimal number of notebooks so that their personal search techniques are unimpeded; however, I must recommend students start an individual notebook for each class and then to bind those into stacks based on each semester. This will sequester the data from a lot of your other Evernote endeavors, ensuring a better level of organization for your classwork (as well as a definitive way of recalling an entire semester's worth of data). GrumpyMonkey's link to shared notebooks makes this even more attractive, because you will likely encounter many people who will take the same class. Imagine being able to help out friends who end up taking the same courses! Granted, I advocate quid pro quo in those scenarios.
As to how you actually take notes is something very personal, but I will say Evernote has great shortcuts for generating well-structured outlines. Utilizing tables can give your notes a strong visual enhancement, but I personally prefer swiftness when taking notes—especially during lectures and seminars. You don't want to commit too much to organizing or you will miss the juicy content. Learn the easy shortcuts. When you create a bullet list, use tab to indent and shift+tab (or return) to return to the margin. This will give your notes a great form that translates well to mobile devices. I would take all my notes like this on my laptop, then on my bus commutes I would review them on my iPhone.
A rat can't clap during a symphony Why?
It's little baby rat hands are too pathetic
It's not proper
Rats don't go to symphonies
Learn to tab & learn to love it. Keep the rat from clapping during your symphony. Embrace the tabby cat.
Citations. They are just… Oh my lord. They are my bane. I would have a paper that I would be writing, and I'd literally stop and weep because I was so inept when it came to effectively (quickly) compiling the works I'd cited. I know there are tons of "citation machines," but merely maintaing every single source can be so overwhelming throughout the process of synthesizing your own ideas.
Sooo~ What I've been doing instead is using my iPhone to just take pictures of the bibliographical information—usually at the beginnings of most books. I just start a note with a title BIBLIOGRAPHY for X Paper, and collect them there. So long as you're vigilant, your life will be made much easier once you begin cultivating your works cited from this note. This is admittedly inefficient (charlatan!!!) because just typing the info out immediately would lead to less work. However, this is how I do it, and sometimes it is best to submit to your quirks for improved fluidity in your workflow.
I use the same strategy with quotes / passages. I do this instead of highlighting. Not only do I get to carry with me, permanently, a salient piece of text, but when I go to write my paper, it is simple to organize the pictures of passages chronologically, and the thesis I'd perhaps not solidified prior to my research then crystallizes rapidly. As GrumpyMonkey said, the OCR capabilities of Evernote also enable you to sift with efficiency should you need to find an elusive passage. Win/Win~
WebClipper. This thing is incredible. Doing research papers when the Internet was first emerging as a standard commodity for higher education was frustrating. The entire process of citing information from the Internet was anathema to all, due to its frequently illicit nature. It still is, thanks to copyright laws that are so highly contested and equivocal. The WebClipper changes this, I think. Not only does it pull articles with ease, but it validates the usage of more dynamic content by stabilizing and freezing it for easy reference in Evernote.
What I mean by dynamic content is that you can go to Twitter or this forum, clip salient discussions, and have a better, permanent document that can be attributed to your research. I much prefer this instead of, say, screen capping, copy pasting, or downloading source codes and all the content yourself.
More progressive professors might enjoy having a PDF compilation of such referenced web content, and readers of your research will, too. I believe this will soon become a standard activity for a researcher who would like to preserve the best representation of her sleuthing.
If your professors are as tangential as mine were, you will often have moments in your note taking where you're like "what are they talking about? this sounds important but it doesn't belong here! NO! you're ruining my beautiful floooow!"
So have one note open that acts as the sort of core for a lecture, and another note open to catch the weird little crumbs that tend to be shed by teachers. Those crumbs tend to be quite important, too. Keep them. Keep them and eat them.
Treat your syllabi with reverence. Scan them, retype them, just put them in your Evernote and keep them available in a very visible place that you will see that is not hidden. This will save you so much angst when it comes to knowing what you should be doing, when you should be doing it, when it is due, what criteria to fill for projects, and more. Some dedicated people will input these things into their calendar personally, but having the original document is ideal, especially in circumstances where deadlines are misinterpreted.
Ugh, I could keep going, but this is already too long. I hope it helps someone!ヽ(・ω・ヽ)