Make sure you look at the specs of the program you are trying to use - you could have the wrong system software and/or Mac ROMs for that program.
So, if you have a program that requires a 32 bit clean system, then it is likely not going to work on a Mac with 256K ROMs (Mac II, Mac IIx, etc.) Likewise, a program that is making jumps directly into the Mac ROM is not going to work one some Mac models.
Now, to be clear, there are some programs that only work on certain Mac models. As far as I know everything else ever made for the Macintosh works. It was not possible to make either of these work and still have the Amiga function in the background, so these two programs were not supported. Macsbug by Apple, and another program (I don't recall the name of it) that used the MMU to handle memory management. When the last version of FUSION was released, there were only two programs that were known to not work with it. FUSION came from the Mac emulation that was released for the EMPLANT hardware that I created. I also made FUSION-PC, which was a PC version that today runs circles around any real or FPGA based Amiga when using modern PC hardware. I am the creator of FUSION, the fastest and most compatible color Macintosh emulator ever made for the Amiga. Gunnar asked that a new thread be started discussing Mac emulators. Welcome to the Apollo Forum This forum is for people interested in the APOLLO CPU.