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?