I am also looking for something like this. RomLister does not work because it only creates lists to use in various frontends. I want a program that will list the ROMs I have by name and be able to delete them from my hard drive.
There is a way to do this in romlister. A little convoluted, but doable.
In ROMLister, load in your XML file for the version of MAME you have.
Then, also in settings and tools, click the "rom scan utility" button. It will scan your hard drive and take your existing rom set and build a new XML file off the physical zips that you have. Now you have a 1:1 XML file and set of zip files.
From the main romlister screen, click on "list all roms".
You now have an interactive list that you can delete rom.
Delete any rom that you don't want out of that list.
When you're finished, just export your list to a batch file, one in which you MOVE the roms that are still in your list to a new folder on your hard drive. Execute that batch file and then you can delete whatever is remaining.
There's a tutorial for batch files here:
http://wiki.arcadecontrols.com/wiki/RL_tutorial_batchFilesedit: start with step 7 of the moving roms tutorial.
But jeeze, don't do it *all* by hand! ROMLister's job is to help trim down the list of roms into something manageable. Use it, THEN trim down the fat by hand if you still need to.