It kind of annoys me that we've got all these "kind-of, sort-of" related stack exchange sites for programming and whether one question belongs on Stack Overflow, or Programmers.SE or cstheory.SE or whatever is often quite hit-and-miss.

But then, on the other hand, you have tags on Stack Overflow that are almost separate sites in and of themselves. Usually this happens when companies start using Stack Overflow as the defacto support forum for their product (a lot of Google stuff uses this, e.g. http://stackoverflow.com/questions/tagged/google-apps-script or http://stackoverflow.com/questions/tagged/android etc)