Hi,
Just to push in the same direction, I have 2 C2duo, both running amd64
Debian, one with a custom kernel compiled with the "c2duo - newer-xeon"
arch instead of the generic "x86-64" which is the defaut. (can't tell
the difference though...)
FlashPlayer is already available for native amd64 (not talking about the
nspluginwrapper thing) in debian-multimedia (experimental only for now,
but working better already than the aforementioned solution). Free
alternatives are available too (swfdec, gnash...) for amd64.
For java the icedtea jre and plug-in is working ok for me, and Sun
announced a linux native x86-64 build of their browser plug-in for the
next update (available as a beta already).
AMD64 is no longer limited for a desktop user, if ia32 is absolutely
required there's always a way round the problem, like static packages
(Skype...), chroot, ia32libs or even a virtual machine.