OK, I think I figured it out. Thanks for the tip Cananas...I quite like the no-intro naming mentality.
OK, so here's the secret to life, the universe, and everything...
OrganicJerk you are halfway there. Like you did...rename your CRC named snaps to the GoodTools format, using the DAT file from romcenter.
Now...open up the romcenter.exe, and load the same DAT file as your database. Add your local ROM directory as your path. Now you should see a crap load of yellow ROM files with the "bad file name..." error, as well as "bad rom name error". Ignore the latter, as they are just extension changes, and I think if you rename them, you may very well run into problems with your emulator.
However, sort your ROM list by error message, then right-click on all the "bad file name" ROMS, advanced, rename files.
That should do it. I've now got 100% matching snaps to roms.