I think it would be useful to have parent child relationship information in the .dat files.
Just pack together all versions of a single disc.

For example

Final Fantasy IX (Disc 1)
  Final Fantasy IX (Europe) (Disc 1).bin
  Final Fantasy IX (Europe) (Disc 1).cue

  Final Fantasy IX (France) (Disc 1).bin
  Final Fantasy IX (France) (Disc 1).cue
  
  Final Fantasy IX (Germany) (Disc 1).bin
  Final Fantasy IX (Germany) (Disc 1).cue
  
  Final Fantasy IX (Italy) (Disc 1).bin
  Final Fantasy IX (Italy) (Disc 1).cue
  
  Final Fantasy IX (Spain) (Disc 1).bin
  Final Fantasy IX (Spain) (Disc 1).cue
  
  Final Fantasy IX (USA) (Disc 1) (v1.0).bin
  Final Fantasy IX (USA) (Disc 1) (v1.0).cue
  
  Final Fantasy IX (USA) (Disc 1) (v1.1).bin
  Final Fantasy IX (USA) (Disc 1) (v1.1).cue

Is anyone working on this?

Maybe I wasn't very clear about what I meant.
Now after playing around with the DAT files myself I know how to do it.

So I want to suggest that the same Discs or very similar ones should be grouped together (if it's basically the same game just a different version), this way the user can create merged or split sets.
This can be done with the "cloneof" attribute for the game entry.

All that needs to be done is create a new game entry with no roms at all, this is our group.
Then use the groups name as "cloneof" attribute to group them together, this works with clrmamepro.

Here is modified DAT file I made, it also includes the tool I wrote for this very purpose.
http://www.mediafire.com/download.php?75ux4rjca7j58xp

Parent/Child relationship can be between the 1st master and remasters (re-releases) of the "same" title and region.

What you are talking of is "grouping" of discs with similar contents smile

Using a "cloneof"-attribute in this case sounds wrong IMHO, but if this is the way clrmamepro works to group similar items then its fine i guess ))

PX-760A (+30), PX-W4824TA (+98), GSA-H42L (+667), GDR-8164B (+102), SH-D162D (+6), SOHD-167T (+12)