TITLE: How do you keep your research notes organized?
QUESTION [118 upvotes]: One of the things I struggle with most in doing research is keeping my notes organized. Since research tends to do a lot of branching, keeping notes in a linear fashion seems useless to me. On the other hand, this means that I end up with several notebooks that have ideas and dead-ends everywhere. Then if I want to piece parts together, or if I eventually want to go back and re-investigate what looked like a dead-end at the time -- perhaps because I have learned some new tool -- it takes me a long time to find what I am looking for. How do other people surmount these obstacles?

REPLY [2 votes]: I use a tablet notebook running Windows 7, so my way is probably not what you're looking for. 
I take handwritten notes (my handwriting is rather neat) using Windows Journal. I can save it directly to PDF (if I need to share the notes), or save it in its original format for convenience of editing. Almost all my notes now reside on my hard disk (portability).
I use Mindjet MindManager to create a mindmap of how the notes pertaining to a particular broad topic are related (in content, and time-wise, as further notes are taken). I can easily put in direct (hyper)links to these files right in the mindmap, which is a nice feature since the file is a click away on the map. I can add more notes, web links etc. to the mindmap, as required. I can also link to preprints, journal articles, ebooks (even ebook pages/sections, as I can link to ebook bookmarks on the map) on my notebook, so the note- taking and keeping become quite dynamic, which is nice. With MindConnect, you can also sync the maps online, and even share them with others, or brainstorm with other people on a map online. 
I can easily hand-annotate PDF files using PDF Annotator. With a library of ebooks, imagine the web of information you can create right on your computer, in a mindmap. It's quite fantastic. Lots of possibilities there!