For the past few weeks, I've been trying Freemind and Evernote. Freemind is a mind-mapping program useful for taking notes and brainstorming. I've also been using this to handle a to-do list using the 4 quadrant approach (Sort tasks by importance AND due date) + 5 minute rule (if it takes less than 5 minutes, do it now) although it's not specifically meant for that purpose. I'm trying out Remember The Milk to see if it works better (A possible review later on).
Evernote is a notetaking application. It comes with a handy visual recognition system and automatic online-backup of the notes. I did find it annoying that I had to register (free!) to user the program. It has a wide variety of features and it's certainly better than my notepad approach to taking notes!
I do certainly wish that the good features of both of these programs could be combined into something better. I've been taking notes on this idea in evernote and brainstorming about it in freemind, so you might see a possible program (Definetly free and most likely under an open source license) for this task comming out in the near future.