I use tiddlywikis as an organizational tool. I have one that I keep a list of all my current projects in, their current status, links to their cases in our webmail/support system, and links to individual project wiki files.
For large projects, where a simple word document with a statement of work is insufficient, I create a project wiki. These usually include todo sections, lists of feedback with corrected items crossed out, specifications for complicated interactions, etc. These usually also have a link to the support case, as well. These come in REALLY handy when you suddenly get a promotion and need to hand a project off to somebody else, or when you have several month gaps between working on a given project.
I've seen a lot of FLOSS projects use wikis for both user documentation and developer documentation. Some even have integration for forums associated with the wiki. Ultimately, you have to decide what will work best for you. For example, a User wiki has to be visible outside your corporate firewall, but a developer wiki can be on most any purely internal server.