I have tried quite several solutions to organize the projects I worked on, the tips accumulated, and the notes I took from seminars. The goal is to have something portable, cross-platform (different OSs, mobile), neat, efficient, easy to keep things organized, and free!
The solutions I tried include wiki-based content manage systems, MoinMoin, DokuWiki, AbstractSpoon TodoList, WorkFlowy, Microsoft OneNote, Evernote, and a few others. I ended up with Dynalist for taking personal notes and knowledge organization.
I like many of the features of the free Dynalist version that meet the majority of my needs (comparison can be found here ), and it surprisingly supports some LaTeX syntax for easy math formula typesetting.
Only two things that do not have a good workaround with Dynalist. First, no version control in the free version. Second, it is not suitable for collaboration, although sharing is possible. These are probably better implemented in a wiki system.