Dealing with large collections of MAME and console roms can be a real pain in the neck, especially when it comes to clones, alternate versions, and non-working roms.
One particularly painful problem is that of the various MAME clones. Lets look at Pac-Man/Puckman for an example.
Now that is one "Original" game, and 11 clones. That wouldn't be much of a problem except for the fact that the version everyone actually wants to play (Pac-Man), is one of the clones. You need the original in order to play the clones. So in order to play Pac-Man you have to have Puckman clogging up your game menu as well.
Lets look at one more common example before I go on to provide the solution to the problem.
The "Original" version of Wonderboy in Monster Land (and many other Sega titles) does not work. Only a clone version works. So in order to play the working clone, you have to have the non-working "original" clogging up your game menu.
Mame32 does provide some pretty good sorting abilities. You can view only "original" games, or only "available" games, and many other options. But none of them provide the solution of hiding clones, except for the games that don't have working "originals" (and hiding the "original" versions in that case).
Deleting all unneeded clones is a big step in the right direction. But that still leaves you with a bunch of duplicate games to clog up your menu system. You are going to have Pac-Man and Puckman, and tons of non-working originals just waiting to be accidently selected.
The solution is really rather simple. All you have to do is dump the files from the "original" game into the zip archive of the "clone" game (when both archives have a file with the same name, keep the one that was already in the clone archive). Then you can delete the "original" and the clone will remain on your menu, while the useless "originals" will be gone. This allows you to just keep one working version of each game, and get rid of all the useless duplicates. This doesn't just work for MAME, it works for most arcade emulators that use "original" and "clone" archives.
This is also usefull for people who are concerned about legality. Perhaps you do own* a US version X-Men Vs. Street Fighter PCB, thus giving you the legal right to play that game. But you don't own the "Euro" version, which is the "original" under MAME. You can use the same method described above to create a single legal archive of the ROMs that are actually contained on your boardset.
*In my case I do own a Ring King boardset, but I do not own "King of Boxer", which is the "original" version under MAME.