Is there any real difference between AMD64 and Intel’s CT?
Let Intel answer that question. From here:
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.
In other words, there isn’t any more difference between AMD64 and Intel’s CT than already exists between Intel and AMD processors, and no serious commercial program is going to require that SSE3 or hyperthreading be used.