I have music lying on my desktop and in my downloads and Music folders. Similarly, I have .odt files lying all over my home folder (mainly desktop). Is there a tool (preferably GUI so my parents can use it later) that sorts all these files into folders (/music, /docs, /others) for some peace of mind?
A clear (at least in your head) organization that you stick to as you go along is far and away the best solution. Any automated moving of files is almost certainly going to make more mess than it cleans up. There will be issues with name clobbering, and any deviation you try to make will just end up as more mess when it gets processed as well.
It would be really easy (as in just a couple of lines) to write a script to find and relocate files based on their extensions, but you would have to be much more specific with your question to get a good example of this.
I largely agree with Caleb's answer, but just for a little practice I wrote a shell-script for the task (by no mean does this imply that I'm a master of shell-scripting so comments welcomed).
Here is the script (it's a few dozen lines long so I'm making it a link) https://gist.github.com/1160707
To use the script:
To save from running commands, you can make an application shortcut on the desktop to run the script by double clicking. How to do this depends on your desktop, but I'm sure it's fairly easy if you are using something like GNOME or KDE.
For a little fanciness I make the script show a desktop notification when done.