I wrote a quick DOS command-line utility to do something like this. It searches through all of the ROMS in a given folder, and then copies my "preferred" dump of each game into another folder.
My preferred ROM for a game is determined as follows...
1) Ignore any ROM with "hack" in the title
2) Find my preferred country dumps (U...if none exists, E...if none exists, J...else other)
3) From all dumps in my preferred country, copy the [!] (known good dump) version to the other folder.
3a) If there is no [!] version, copy the version without any [] codes.
3b) If there is no version without [] codes, just copy the first one found.
Essentially, this just leaves me with one good dump of each game (except for hacked games), with english-language versions having precedence. And it works for any of the GoodCode sets.
I figured this was a pretty useful utility, and was surprised that I could not find anything else out there to do this. After all, do I really need to scroll through 15 versions of the same game in my FE?
Anyway, if this the kind of utility you were looking for? If so, I could post it on the web.