I ran into the same issue. I looked at a few utilities, but the ones I found didn't do exactly what I wanted them to. I ended up writing a small utility myself that lets me "rank" each of the descriptors (like [!] or (4)), and copies the "best" version of every ROM (based on assigned ranks) to a new folder.
I then realized the problem with artwork files haveing exact names, so I added an option so that any roms with matching artwork can be considered "best."
If you want to give it a shot, PM me your email address and I'll send it to you. Just remember that no one but myself has used this to date, so testing is minimal and there are no instructions currently (and it's ugly). That said, it doesn't delete any files (just copies from your ROM folder to another folder you desginate), so there's no file risk in using this. However, if duplicates exist in the destination directory, it will overwrite then. That just reminds me that I never included a check to make sure the source and destination are different dicectories.
So there's not much risk... aside from that fact that you'll be running unknown software from a stranger.
