Windows Server 2003 is licensed by core. Enterprise edition supports 8 SMP cores. With new CPUs supporting 6 cores with hyperthreading, you end up with 12 cores – 4 of which will not be used by the OS!!!! This can be a bummer if you are running SQL Server Enterprise Edition because it will use only the cores supported by the OS (i.e. 8, not the 12 that you have)…. ooops!
On the other hand Server 2008 R2, the licensing is by X64 sockets. So a single CPU with 12 cores will use all of them with any edition (including Web and Standard). In short, you will get more thru-put with Server 2008 R2 Standard Edition then you would with Server 2003 Enterprise Edition. If you go for a fancy box, you could be running 48 cores on 4 x64 sockets with Server 2008 R2 Standard Edition (something that required the Data Center Edition with Server 2003).