Keith, as far as Quasars go, there is a series of papers by Roberto Terlevich and collaborators suggesting that at least some sources classified as Seyfert 2 galaxies and quasars are not powered by non-thermal radiation from black holes but by a number of compact supernova remnants from massive stars. Roberto moved to Mexico some years ago and I don't know whether he is still working on this.

Pulsars are a case where the basic physics is pretty well understood, and there is consensius about the basic components, but its magnetic fields and general relativity, so in detail there is quite a lot of discussion about the nature of the emission and the details of the origin of the rotating neutron stars.