It's tough to really say what's best, but I stick with the default number of CSs. In my mind, 2k tested and balanced the game based on those default settings, so I'll stick to them.
On the one hand, for a fair game, you need a good number of CSs for the sake of those Civs that gain bonuses with them on the map. You also need enough so it is possible to gain a diplomatic victory, as well as majorities to pass resolutions.You also need enough so that some civs could attack them early enough in the game. And you also need enough CSs to go around (It's no fun when one civ hogs all the CSs for himself, other civs should be able to make buddies with at least one CS. And attacking a CS is a great way to annoy rival Civs who promised to protect it.
On the other hand, CSs, in general, take up space and get in the way of the placement of a perfect city. They only seem to defend their close proximity, so their usefulness as an ally in wartime is not as you'd expect.
There are also problems with CSs on specific maps.
I only play Continents or ContinentsPlus so I'll use them as examples.
In Continents, I'd say CSs are generally spread out, but that means they get in the way on the mainland. In ContinentsPlus, almost all are spawned off the mainland on islands, which gives you lots of room on the mainland to expand and place your cities in the best spots, but the early game map feels empty since other civs are too far away for an early war, and you have no CS to get a first land trade route.