I have a new favorite piece of software called Check Off. It's nothing fancy, but it's dead useful. I am an inveterate list maker, and for some time now I've been using Stickies to post virtual to-do lists on my Mac. However, this is unsatisfying to me because I can't cross off a finished item. I can delete it, but then I don't get the satisfaction of seeing all my completed items. Check Off lets you, guess what, check off what you have done, so I just check off things and at the end of the day delete the finished tasks. You can also create folders for sets of tasks. This makes it easy to focus on "stuff to finish this weekend" or "dissertation tasks."
You can download Check Off here (if you have a Mac).