If you want to remove masters/clones. The option remove "only masters" removes the clones and "only clones" removes the masters. The way I see things, if I want to remove masters I would select "remove > masters" and all masters would be removed.
Now to spice things up. An option to remove clones only when a master exists would be handy. I have an ArcadeVGA mounted horizontally so I remove all vertical games from my list. I also have a script that checks INI files created by avres and builds a mame32 INI file of roms with "resolution auto" (i.e. no matching ArcadeVGA resolution). I then import this into the game list editor, save as MNL and use it to exclude roms from my main game list. Where I run into problems is with games like Scramble because the master has an different and incompatible resolution to some of the clones which have compatible resolutions. Non-working masters and working clones is another scenario (although I haven't encountered this myself).
It would also be nice to remove roms using multiple keywords rather than one keyword at a time. Similar to the existing option "remove by name content". Perhaps it could be modified to accept a comma separated list of keywords. I remove keywords such as "golf, tennis, adult, mahjong" etc. Being able to execute this in one action would be much easier than doing each keyword individually.
In much the same vein it would be nice to remove roms by genre using check boxes rather than a drop down list. At the moment the process to remove all the puzzle, maze, sport and *mature* etc roms is rather time consuming. A single dialog that displayed the genres and allowed selection using check boxes would speed up the process immensely. In one action I could remove all that I didn't want.
Cheers,
Matt