Yeah, I'm not sure who mentioned anything about anyone
changing a
standard. I thought Demon-Seed was just talking about displaying them in his FE.
I believe the way DK does it now is that it just strips off the extra characters, leaving a bunch of listitems that look exactly the same when in fact they are different ROMs. I'm not sure this is what Demon-Seed is looking for.
MAMEWAH I don't think has this ability for console ROMs, since there isn't a concept of parent/clone relationships in the DATs for them. AFAIK, that's the closets thing MAMEWAH has to this.
Kymaera can do pretty much anything you want, but is a little buggy to get going yet. I'm not sure about any other FE.
"tr00t" about the goodtools being able to set your list back to the way it was. That means no matter how much you f-up your ROMs, restoring them is only a click away

You could implement essentially the same thing as a parent/clone relationship with console ROMs by just coming up with a 'standard' and sort your ROMs that way. For example, say, the "parent" would be everything with a "[!]" and is the latest version (no matter what country it's from). Then any "clones" would just come under that. Older versions, different country origins, etc.
Whatever it is, the hardest part would be agreeing on a set of rules. After that, making a DAT file for that is the easy part...
-Steve