I hand-filtered all my sets down by hand, keeping the best one using the following priorities:
1) Working?
2) In English?
3) Is it a parent rom? (kept even if not working as needed to support a working clone)
3) If the game has a unique quality (ie. a 'fast hack', variations of SF2, different characters etc.)
There are other considerations I made such as if there was no English release, or if I remember a game by a certain name but the parent rom was different (eg. Ninja Gaiden was a parent, but I remember playing it as 'Shadow Warriors' as a kid).
Once done, I unzipped and re-compressed all my sets, cutting the space they need on the hard drive by over 100Gb fro my initial sets.