R2 of Windows 2003 of course. I'm hoping in the Vista craze that this release doesn't get ignored because it has a lot of cool features that you can use without doing application validation all over again because it builds on top of Windows 2003 SP1.
I think it was a good design choice to do it that way. You install Windows 2003 SP1 (essentially) then insert disc 2 and it adds on all the specific R2 features. If you have some sort of application regression that some 3rd party won't support because they've never heard of R2, don't use disc 2 and try it again. If it is repeatable with just disc 1, it's something that would affect Windows 2003 SP1 also.