I try to follow the PSP 2.1 process when possible. It really helps me keep a focus on not skipping important, but less exciting, portions of a project. Usually this is design and design review for small projects.
To keep track of time you can use the PSP Dashboard, which has a bunch of built in features and scripts that help you follow the process.
If you are just looking for a time-tracking tool, I also like http://slimtimer.com. It can also do some decent reports.
