If people are fans of the GTD stuff, for programmers who use eclipse as their main IDE I would highly recommend the Mylyn plugin. By default it should come with eclipse 3.3

http://www.eclipse.org/mylyn/

"Mylyn monitors your work activity to identify information relevant to the task-at-hand, and uses this task context to focus the Eclipse UI on the interesting information, hide the uninteresting, and automatically find what's related."