I'm currently using the Q6700 with Windows XP, and Ubuntu Server 8.04 both 64-Bit versions. So I don't see why it would not be able to run Server 2003.
Hope this helps.
Intel Q6600 is a quad-core 64-bit VT enabled processor and Windows Server 2003 R2 64-bit is in it's certified OS list so it will run just fine. For further details, you can also refer to the following URLs:
Intel Go Green, Save The Environment!