I prefer split sets as it allows me to keep the unwanted clones out of my menus, while putting in the few clones that I do want.
One neat trick when you want a clone without the parent is to add the contents of the parent romset into the clone zip. That will make the clone show up and work, but the parent won't be on the list. That is a great solution for games like Pac-Man and those Sega games that have non-working parents but working clones.
Also good if you just prefer one of the clone sets. Not that I can even tell the difference between most of them. I don't really know of a lot of major differences between clones and parents (aside from title differences).
Here are the ones I DO know.
Nibbler - Clone keeps your snake full length after you die, parent doesn't.
The End - One version has you on top of the shields, the other underneath.
Pleiads - Tehkan version doesn't give you as many/fast shots on screen.
Donkey Kong - The barrels won't turn onto a ladder when you are one it, if you are near the top (Japan version).
Anybody else know any differences? Any good websites on this (The main differences between William's versions seems to be default difficulty, which you can change anyway).