Personal Software Process tools
I'm a big fan of Watts Humphrey's Personal Software Process. I've learned a lot about how I actually develop software and have made some improvements based on actual data about my work. The downside is the effort involved in the data collection and analysis, so eventually I wrote some custom tools.
The easiest was a Lines of Code counter. It counts logical lines in Java source code files and can be used in a terminal or with the supplied GUI.
Then I made a timelog tool with a built-in timer/stopwatch. This took a bit of work to figure out how to manage the threads. I also revised it several times to make the user interaction as smooth as possible.
Finally, to tie everything together, there's a summarizing tool that is essentially a database of all your data with integrated metric calculations.