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I use plaintext files edited with VIM for web-related notes, and organizing thoughts.
And finally I use a LiveScribe digital pen for lecture notes and jotting things down while reading printed papers & books.
I think what people often use notes for is as a surrogate memory. There's a desire to search through them for that one gem which will trigger you to remember all that you once knew. Or worse, it's a search for that part where you can just relive whatever experience you thought should have taught you it the first time, but didn't. To this end we have organizers and smart pens and the like. I might be jaded but they all seem like so many fancy gadgets that all seek to solve a very orthogonal problem.
I disagree with the "note taking habit" greatly because I think it's in your best interest to learn instead of memorize. By which I mean that if you're truly studying something, the goal must be to enact some sort of change in parts of your life far beyond just what you can regurgitate. It's starkly contradictory to a lot of what everyone seems to practice in education, and my adherence to it has cost me in graded performance, but it's also placed me far above a lot of my peers in both comprehension and success.
My goal when learning is building my own, real mind maps. Every thing I ingest has to be processed, extended, applied, and connected to other things. You have to act, not just listen and listen more than notate.
In classes that translates to a lot of questions that go beyond the scope of the material and great conversations with professors (in our own time). In information consumption, it translates to a much slower rate of consumption (helped by a lot of filtration) where action items are not just stored up but actively performed while things are still fresh and exciting.
In short, I try to maintain a distaste for what you might call "consumption mode flow". Learning is atomic and it takes effort to decompartmentalize the things you read into real effects in your life. That decompartmentalization is the best notation method possible, though. If you want to remember something important, make sure it rubs up against everything you do every day. If it's not so important, why write it down?
(Also, for voting purposes, pen and paper is best. I find this style of thought is aided by not being able to erase.)
This is somewhat tangential to what you're looking for, but I often get a lot of questions in classes about why I'm never, ever taking notes. It's firstly not quite true and secondly something sometimes difficult for people to understand. I think what people often use notes for is as a surrogate memory. There's a desire to search through them for that one gem which will trigger you to remember all that you once knew.…
I've actually tried many different software applications, but I've found that when I write something down, I'm forced to think about it a bit, and I remember/learn better. With software, its too easy to just copy, paste, and forget. I'm also a very visual learner. My notebooks are full of diagrams, pictures, arrows and other text annotations. I've yet to find a piece of software that easily lets me do that.
For actually remembering information, note taking is a good first step, but I usually don't keep those notes. To actually assimilate knowledge you've got to to take it in, put it in the context of the rest of your knowledge, contrast it with other things, and ultimately use it to produce something.
I think Evernote is pretty decent for this. I just use the web version, but because of the work I do, I have to read a ton of documents online and usually want to refer to them later. Evernote helps because I can use the web clipper to save whatever I am looking at and then tag it and even write some notes on it. Then later I can fire up the desktop application and go through my notes. I believe the mobile versions a…