Another thing you can do in Mame32 (frontends + regular Mame might have the option too) is to sort them by the "Originals" category that is on the left. This will only show the parent ROMs, or in the case of ROMs where only a clone or bootleg works (such as Choplifter in the old version of Mame32 that I use), it will show the working ROM.
This is useful if you just don't want the clones/bootlegs/revision ROMs cluttering up your game list. If you are looking to save hard drive space it won't help of course, because it doesn't actually delete anything.
If there was a way to generate a text list of the "Originals", you could use a batch file to copy that entire list of "Originals" ROMs to another folder, then delete the original ROMs folder.
For example, if you could somehow generate a text list of the "Originals" ROMs (maybe clrmame or certain frontends can do this?), and it looked something like this:
abc.zip
def.zip
ghi.zip
jkl.zip
mno.zip
pqr.zip
stu.zip
vwx.zip
yz1.zip
Of course it would be a really long list and have real ROM names, but anyway ... using a spreadsheet like Excel, you can easily and quickly make a list that looks like this:
copy abc.zip c:\originals
copy def.zip c:\originals
copy ghi.zip c:\originals
copy jkl.zip c:\originals
copy mno.zip c:\originals
copy pqr.zip c:\originals
copy stu.zip c:\originals
copy vwx.zip c:\originals
copy yz1.zip c:\originals
Paste that into Notepad, save it as a batch file, place it in your ROMs directory and run it, which will give you a new folder (c:\originals) which only contains the parent or working ROMs. In case of the few games where the clone or bootleg works but the parent doesn't, you would have to go back in and copy those non-working parent ROMs to your new folder. Then delete your old ROMs folder, and replace it with your new ROMs folder.
This all assumes there is a way to generate a text list of the "Originals", which I'm not even sure is possible.