I recently started using a personal version of the MediaWiki software for my notes. It's free, easy to use, and available from http://www.chsoftware.net/en/useware/wos/wos.htm.

I keep a blog in the wiki where my daily notes go but that blog refers to 'project' pages, 'tool' pages, and 'process' pages. I have templates for regression tests, the results of which go into my wiki. I also have a glossary (which was great when I started a new job, recently) and a list of people (with links to the projects on which they're working). Even better: if I don't remember where I've put some notes, I can search. I've come to like this method of note taking so much that I have started taking my home notes on a thumb drive running this same software.