Brought to you by the folks over at Lifehacker is a nice little handful of scripts (bash and python) that makes simple TODO managing not so difficult. Todo.txt is a nice bash script that manages todo lists in a simple plain text fashion. Nothing too complicated. It even allows you to break things down into projects, and such too. Very nifty. Windows users will probably want to grab a copy of cygwin as well.
In addition, they also have a nifty little Python script called Birdseye that can give you a nice overview of your projects.