Im currently doing snaps for gensAvga and zsnesw.
If use use mamewah ,it renames the snapshot for you.
ie ZSNES creates a snapshot called image.pcx which is renamed to the rom name with the picture extention.
In gens its ROMNAME_000.bmp renamed to romname which iis then put in my snaps dir.
The only hitch is sometimes inside the goodgens named zipped rom is the badly named smd file ie Alldn instead of Alladin_[!].The snapshot taken is then the smd named file not the proper goodgen named zip file.
All I do then is go:
Right Click on good rom name ,rename , copy the highlighted rom name.
Go to bad snapshot file , right click , rename ,paste . now you have snapshot the same name as rom.
Sounds messy but u get quick if u have the two folder displayed at the same time and all your snapshots are done in alpha order.
Maybe someone out there knows of a way to rename files in the zip to the same name as the zip?

? then its easy using Mamewah ,,,just press f12!