I opened http://bugs.python.org/issue7146 ([PATCH] platform.uname()[4] returns
'amd64' on Windows and 'x86-64' on Linux) and contributed a patch.

pjenvey is right: setuptools just relies on distutils which relies on os.uname
which relies on the underlying operating system.  Unfortunately if you are on
the amd64 architecture then Linux returns 'x86-64' while Windows returns
'amd64'.  It seems to me that the Lib/platform.py module should unify this so
that you get the same string denoting that particular 64-bit CPU architecture
regardless of what operating system you are on.  I guess this calls for a patch
to Lib/platform.py to get the return value from invoking 'uname' on Linux,
checking if the answer was 'x86-64' and replacing it with 'amd64'?

This isn't a setuptools problem. distutils determines this name 
(distutils.utils.get_platform) via os.uname (so arguably it's the OS's problem?
).

setuptools just uses the distutils for determining the name, and we wouldn't 
want to be out of sync with it anyway

+1

Currently eggs created for amd64 platforms are called x86_64 in the egg
filename. AMD renamed x86_64 to amd64 and asked people to follow suit.
Also Python uses the amd64 nomenclature:
http://mail.python.org/pipermail/python-bugs-list/2006-December/036400.html and
http://mail.python.org/pipermail/python-dev/2008-May/079056.html

As such, to limit end-user confusion eggs should be named amd64 as well instead
of x86_64.