"Running a 64-bit Linux may sound trivial for an open-source operating system, but there is a lot of work to be done. First kernel developers must build a 64-bit kernel and port the necessary drivers, but then there's a truck load of software that may or may not have been written well enough to simply be recompiled to run."

LinuxHardware.org has a very nice writeup on 64-bit Linux and the Opteron, including a rather comprehensive 'Opteron Primer'.  Check it out.