Ask HN: How could I automate the process of cleaning up my folder structure?

Not sure your OS but if you're running anything with a decent shell (eg Linux, BSD, or Mac OS X) you can do this all from the command line. You should be able to do the majority of what you want with a combination of find/while/sed/mv. If the old-to-new naming scheme is too complicated for sed then replace it with a awk/perl/python/ruby.

If you're relatively new to using the command line to do things like this (I'm guessing yes) make sure to backup your documents first. It's very easy to accidentally delete/rename all your files with a couple typos (but don't let that scare you off from learning).

It doesn't help with renaming per se but Belvedere can help keep things organized.

http://lifehacker.com/341950/belvedere-automates-your-self+c...

Try http://www.bulkrenameutility.co.uk/

um.. http://www.hiteksoftware.com/mize/task-scheduler.htm is quite amusing..