I've recently started using FreeMind and I have to say I absolutely love it. Its a great tool and it seems to have the good enough feature set .. so far no complaints!
I've long struggled with using PowerPoint (actually OpenOffice Impress .. but PPT is more a category statement!) to organize even presentations because of the strictly linear nature of the beast. I'm a big whiteboard fan because of the 2D environment it gives me to think with .. and still use a paper notebook for the same purpose when not in front of the whiteboard or when I need to get the results portable. I think FreeMind may be a good alternative to all of that - we'll see.
You may also want to check out this FreeMind demo video.