Pavel's diary

Intel released docs for their x86-64 implementation

Intel released Software Developers' Guide to their 64-bit Extension Technology.

They also published FAQ on their technology. Although mainly PR oriented, the last question and the answer is interesting:

Q9: Is it possible to write software that will run on Intel's processors with 64-bit extension technology, and AMD's 64-bit capable processors?
A9: With both companies designing entirely different architectures, the question is whether the operating system and software ported to each processor will run on the other processor, and the answer is yes in most cases. However, Intel processors support additional features, like the SSE3 instructions and Hyper-Threading Technology, which are not supported on non-Intel platforms. As such, we believe developers will achieve maximum performance and stability by designing specifically for Intel architectures and by taking advantage of Intel's breadth of software tools and enabling services.

So the result from reading this is: although AMD's and Intel's architectures are completely (read entirely) different, you should optimize for AMD64, because it will run on Intel's 64-bit extension technology without problems. You can't do that vice-versa, because Intel added additional instructions to the architecture.