I am using my copy of winUAE with an AMD64 laptop and with Windows XP 64-bit edition. It runs great, much faster than it did under 32 bit windows XP.. I won't post benchmarks because the OS is still under free beta testing and won't see OEM launch until early next year. But you can get a free copy on Microsoft's website.. Now if they'd just make a 64-bit version of winUAE (so I wouldn't have to run the 32 bit app in 64 bit mode)..
If you are a WinUAE developer and you say "BUT! there are no 64 bit apps", have you tried POV-RAY it's already ported to 64-bit..