I've used Keystone in a few projects, and found it very easy to use and modify. After introducing it to other developers and testers, they were able to come up to speed rather quickly and navigate its various forms and reports.
I've written a number of extensions for specific purposes and made modifications, and found it very straightforward. I really hope White Pajamas either sells the product or makes it open so that it won't die on the vine.
Simply put Keystone is the best bug tracking software on the market.
I found it very easy to customize.
An open, cross-platform journaling program.
A scientific plotting package.