I did the same as turnarcades, go through them and take out what you do not want. I have an excell spreadsheet and I go through listing the games I like, there full title, mame command (as I use the command line version), type of game it is, and comments.
Im in the M's right now, when I get done with the list from A-Z everything not on my list as a keeper gets deleted..
The reward in doing this is saving space and probably running into a ton of games you never knew exsisted that you like.
Of course you own every single one of those games rom, so you already knew about them.