They are [almost] totally instruction-set compatible*. They are,
however, still quite different CPUs, so it can make some sense for
some packages to come in differently optimised variants, and certain
"missing" features of current EM64T chips relative to AMD chips mean
the kernel has to do some stuff less efficiently (I/O is Just Better on
AMD chips).
* see:
http://en.wikipedia.org/wiki/EM64T#Differences_between_AMD64_and_EM64T
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