My 1200 came with an Apollo 060 and the Apollo 68060.library of course. So I always used that without giving it a 2nd thought.
Is there something wrong with the Apollo 68060.library?
No. It may be slower and there may be some bugs but I'm not sure the Apollo works properly with any other 68060.library. The Apollo hardware is quirky.
I seem to recall that Thor's library utilizes a very clever wrap-around the 4GB memory map trick to get superfast speed. Which of the other libraries do the same trick?
I hadn't heard that. Do you mean virtually map some code/data to the upper (negative) 32k of addresses so absolute short addressing can be used? What did he put there?
If a person uses WinUAE and they set CPU=68060 then which 68060.library should they use, if any?
And what if they set CPU=68060 + FPU=68882?
(So there are no unimplemented FPU instructions)
I believe UAE will install all the missing instructions of the 68040 or 68060 when these processors are selected. If this is the case, then the answer may be none (installing a 68060.library may be slower). I recommend checking with the UAE documentation though.
Also, does any of this stuff affect OxyPatcher/CyberPatcher ?
OxyPatcher should work with any 68060.library. CyberPatcher may require the P5 68060.library and MuRedox may require the Mu 68060.library but I'm not sure.