So the question of the year is "will Commerce Server run on Windows 2008"? The answer is "YES" with a big BUT you have to wait for Commerce Server SP2 targeted second half of 2008.
To confirm I sent an email to email@example.com and they can't comment as they are in the planing phase so we just have to wait and see :(.
I am pretty sure that .NET 3.5 falls on the same bucket.
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