I thought I'd post my method in hopes that others will explain theirs.
Here's an example of my file structure:
Example .mxm file...
Z:\Maxwell Materials\mxm files\Metals\Aluminum\Annodized Aluminum.mxm
Then the associated texture files would be in this folder...
Z:\Maxwell Materials\mxm files\Metals\Aluminum\Textures
In my case the Z: drive is an external hard drive (a NAS in particular) which can be accessed from multiple computers on my network so no matter what computer I'm on the file paths are the same. I can also backup the files to a portable hard drive which I can take home and have the portable hard drive setup as Z: as well so I can similarly use the same files without changing paths.
Here's a screenshot of how I've got my material's organized...

-Brodie