I am not sure how emulating x86 is different from emulating anything else. Simulating hardware using software does not infringe on intel's rights. I don't think intel's lawsuit has any legs, and it probably only a ploy to try to delay MS to market. So long as MS did everything in clean room (that is didn't borrow any of intel's code) then MS is certainty in the clear.
Emulation has been challenged in court several times before, and so far emulation has always won out. Even in hardware, Cyrix was able to provide x86 compatible hardware without infringing on Intel's right. Being a commercial interest doesn't change things. Patents spell out, in very specific terms, what the technology is and who claims ownership of the intellectual property. Creating software and hardware that is compatible with intel's standards does not infringe on their rights. No one can copy their designs or use their technology without permission, but that doesn't' give Intel the right to control markets or inhibit competitors just because it is inconvenient for them.