All I can think of that I changed was making some civs unplayable. Now half the cities on my map don't show up. Is there any way to fix this, any way to get them back? Was changing that option what in fact did this?
How much-suck. >:(
Just because I don't want the human to be able to play as them doesn't mean I don't want them there at all.

I would just make them playable again. They might still be there, depending on whether you saved after they disappeared or not.

First thing I did was make them playable again -- they're still gone.. :~(

and, yes, I saved after I did it, since I didn't notice until a few minutes later..

This is in the editor not the game right?

By making them unplayable you make them unavailable to everything. Their cities dissapeared because they're no longer available. Then you saved it. That's what went wrong. By saving it and coming back a few minutes later, you can't undo and it's not going to remember where the cities were before because it's like starting over again. They didn't turn invisable, they were deleted. So, you have to place the cities yourself.