I keep my TODO list in a single text file. I have a key bound in my window manager to open it in an editor, and ask me whether to record changes to version control when I close the editor.

The formal is very informal and ad hoc. You can see it here:

http://pastebin.com/f53965a01

I also have an hourly cron jobs that extracts the tasks under "TODAY" and mails them to me.