http://www.zim-wiki.org/ is a personal database I use to organise notes, projects and scripts. Simple cross-note linking and automatic TODO list generation are particularly useful features I use frequently. The 'database' is stored markdown-formatted files that can be easily version controlled and edited from the command line.
I've done some Zim evangelism on HN before ([1], [2]), so I'll merely link those here and mention that I'd love to answer any questions about how I use it.