I think you are right prof, Tinker WUs seem to be fairly close in frame times.. Less than 30 second difference in frame times on identical proteins on my systems right now. The memory intensive WUs seem to be much more in favor of the A64 architecture.
p1477 seems to like cache (and the dothan has 2MB of it). The Abit KV-80 (Via chipset) setup is a 3200+ s754 1MB Clawhammer, running 200x10 2.5-3-3-8. MSI Neo2 (NF3) is a 3200+ s939 512kb Winchester running 240x10 2-2-2-5 DC...and it's only 17sec faster pr frame
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And I am sure the ones that utailize SSE2 see a nice performance boost as well. The double gromacs.
http://www2.newegg.com/Product/Product.asp?Item=N82E16819103439
http://www2.newegg.com/Product/Product.asp?Item=N82E16819103444R
http://www2.newegg.com/Product/Product.asp?Item=N82E16813123240
Though I have no idea if the mobo supports mobiles