Look up SMDB (smoke monster's database). You can download a tool (I forget what it's actually called, I think one is called ROM manager) which reads the SMDB files and compares the hashes to your ROMs and will categorize and rename them for you. It looks for duplicates, unofficial releases/hacks/patches, categorizes them by country (US, EU and Japan largely), and more. It's a pretty nifty tool.

I spent like two hours going through PS1 ROMs and was like "there's got to be a better way!" (insert cheesy black and white infomerical cutaway), started looking up stuff and there it was. Not all game systems are supported (mostly NES, SNES, Genesis/MegaDrive, and a few others) but you can build SMDB "packs" yourself.

I forget if it works on Windows, but I know it works on Linux and it's either a script or a compiled binary, I forget which, but you can definitely script it, I've done so myself since the command string tends to be a bit long.