Also are there any cheap PC's on a PCI card that will work in any of the Amiga or Amiga clones?
Yes, actually. Mr. Hardware Computers sell some. There are also other types kicking around for the general market, too - They're surprisingly common. Bad news is you'll need separate power, mice, drives, etc. - There's no integration on the host side. But at least you'll only have one case.
You could also try to track down a bridgeboard for a classic box - You could run Win95 on it, in theory, but it wouldn't be pretty.
I think MorphOS has Bochs. I'll assume it'll be ported to OS4 once the SDK is released to the public.
EDIT: Oops. I think the Mr. Hardware cards are designed for an ISA slot.
2nd EDIT: An updated version of the Siamese system would be great in today's market, don't you think?