New Tool: KeepNote
One of the big problems I have, as a bioinformatician, is keeping track of all the notes and one off scripts I write. I don't want to use an SVN, because it's just a repository with no organization. I don't want to use a wiki, because it's a huge hassle to maintain for small projects, and I hate using text files.
The compromise, it seems, is to use standards compliant files with a hell of a wrapper around them that does the organization for you, and the one I found is called KeepNote. The project page and downloads can be found at http://rasm.ods.org/keepnote/. The software is available for all major OS (Linux, Mac and even Windows), and can be installed relatively quickly and (for the most part) painlessly. (Linux builds are missing a library in the dependencies, but that can be figured out pretty quickly - just apt-get the missing lib and re-install if you hit this problem.)
While it may not fit everyone's workflow, my few hours of using it have already helped me get my tools organized and assembled in a logical manner, and it's allowed me to remove a load of files from my desktop. There are still bugs with it: I had to manually do some configuration of the the web browser, text editor and such before I could get started, but so far I haven't hit any of the bugs.
It also claims to help you organize notes - which I can clearly see. next time I go to a conference, I'll be using this for recording and organizing the usual 30-40 pages of notes I take.
For me, this falls under the heading of required tools for bioinformaticians and students alike and I look forward to seeing the project evolve and grow.