well.. I was referring to weeding out all the clones by hand.. If you filter them automatically it just filters everything but the parent ROM. In many cases the parent ROM isnt the version you want. It might be in Japanese or something. That's what I meant.
that's a really good point. I think there should be something in controls.dat or somewhere that tells us what the language of the game is in. Certainly, some Japanese games are completely playable to us non-Japanese speakers, but having that type of tag somewhere would be really nice to filter on.
Can you give me an example of a clone/parent where the clone is in English and the Japanese is the parent? I might be able to tweak romlister to find those, but I need something to work with. Otherwise you could use romlister to single out all the clones, and then go through just those by hand to see which ones you want to keep.
easy but time consuming with 4000 games in the list 
That's what romlister can help with.
Either get rid of the games that can't possibly run on your machine first, to trim that big number down to something more manageable by hand, or build a list up specifying the controls that you do have. For example, if you don't have a trackball or spinner, make a list with none of those ROMs in the mix, then import that into Mala and trim it down from there.
-jeff!