I like to organize my information using Anki [1], a spaced reptition system. Anki lets you input information as single flash cards - a question and an answer, and then tag that card by topic(s).

Breaking topics down into questions and answers is a great way to understand infomation deeply for reasons explained in detail at the supermemo website [2]. The crucial added bonus with Anki is that it will manage your memory, quizing you on previously input knowledge at intervals engineered to enhance long term memory.

[1] Anki: http://ankisrs.net/

[2] How to formulate knowledge: http://www.supermemo.com/articles/20rules.htm

(shameless plug)

A short comparison of Evernote, OneNote and iKnow (my company's product)

- http://www.ppcsoft.com/blog/iknow-onenote-evernote.asp

More information

- http://www.ppcsoft.com/blog/ppcsoft-iknow-2011-beta-released...

- http://www.ppcsoft.com/blog/personal-wiki.asp

Summary; Personal wiki/notes desktop application for Windows

(/shameless plug)

If you use a Mac, try:

http://flyingmeat.com/voodoopad/

I tried several of the open-source wiki apps, and then was very happy to pay for VoodooPad. I use it and mindmapping apps quite a bit. I bought a notebook app from Circus Ponies, but I don't open it very often. I use DevonThink Pro Office extensively, and it saves me enormous amounts of time. I also use Emacs orgmode and a few other Mac apps that are probably overkill for most people.

Microsoft OneNote.

Documents, screen clippings, random thoughts, notes, audios/videos - whatever, really - all sorted and searchable. And I have not found a better tool when it comes to handwritten to text conversion as well as full text searching of handwritten notes.

I've been using Catch (www.catch.com) to organize and record just about everything. Their mobile app is pretty well designed, so I'm able to record any random thoughts I'd like to revisit later without much of a hassle.

I have been using thinkery.me, and find it much less cluttered and way faster than Evernote. They also have a nifty bookmarklet to add the current site on your browser to your notes.

I go around for it for a while and found it really useful, but I feel it a bit more a bookmarklet than a library.

I use evernote, dropbox and dokuwiki. Depends on the kind of data and the need to have it available at all times (you know, sometimes you won't be connected to the intertubes.)

orgmode for emacs (http://orgmode.org/) is a swiss army knife for note-taking. If you use emacs, you owe it to yourself to take a look. If you don't use emacs, take a look anyway; I know more that a few people who adopted emacs so as to be able to use orgmode.

I came back to emacs after years with another editor just for org-mode. I can't say enough how it's helped my workflow!