Windows Server 2008 and Windows Server 2008 SP2 are the same operating system, just at a different service pack level (Windows Server 2008 started at the SP1 level because it was released quite a bit after Windows Vista and SP1 was already out).

Windows Server 2008 R2 is the server release of Windows 7, so it's version 6.1 of the O.S.; it introduces quite a lot of new features, because it's actually a new release of the system. This is a good place to start: http://www.microsoft.com/windowsserver2008/en/us/whats-new.aspx.

There are also differences at the GUI level, because WS2008R2 uses the same new GUI introduced with Windows 7 (new taskbar, etc.). Depending on what kind of applications you're developing, they may or may not encounter problems on different O.S. releases; you should definitely check MSDN. The single most important point: Windows Server 2008 R2 exists only for 64-bit platforms, there's no x86 version anymore.