There is effectively NO code difference between SBS 2003 and SBS 2003 R2 operating systems itself apart from some additional windows installable components and a few scripts.
The only siginificant difference is that the System Manager includes "Update Services" know as WSUS (2.0) not the latest WSUS(3.0). WSUS=Windows Software Update Services...Which basicllay speaking allows your server to be a mirrored source for Microsoft updates or depending on how it is configured at least a centralized controller for the ditribution of updates to client PC's in the SBS domain network.
Since WSUS(2.0 or 3.0) is a free download and is installable on the SBS 2003 server anyway. It is really only the management scripting in the R2 version of the System Manager that is different.
It also includes freely available upgrades for Exchnage and other service packs too.
There is also a Windows Server 2003 SP2 which can be applied to either and is independent of the R2 release.
I hope that helps