I have over 3TB of very unorganized files, and it's been hanging over my head for a while to completely organize them.

I'm looking for a program, I don't even know if you would a call it a file manager, that would help me with this daunting task. I'm looking for something that has an interface to keep me focused on stepping through every file in the file system, and keeping track of all the files that I've viewed so far in the organization process.

It would maintain a "master directory structure" that you wish to achieve in the end. On first run of an "organization project" it would ask you to create the top level directories (audio, images, documents, code, configs, binaries etc.), and it would make sure that by the end of the organization process, all other files in the filesystem have ended up in some sub-directory of the "master directory structure", which is the goal of the operation.

Does any one know of some software that can help me with this, or some interesting ways to use common file managers for massive manual organization?

Honestly I would create a single folder called TODO and put everything in it (in the root of the drive). Then start organizing. Create folders and move the data out of the TODO folder organizing it. When the TODO folder is empty you're done.

As far as programs which would so specifically what you're looking for I know of none.

SAM

4pane is a simple GTK based manager worth checking out. It is useful if you just want to stare at a load of files like you would in My Computer. Depending on the distro and window manager you use, this might help you out.
Take the earlier advice on putting everything into a "to sort" folder. I label mine "unsorted" and go from there. Good luck!