Some of the things that you need to consider before upgrading your Windows 2003 Domain to Windows 2008/2008 R2 Domain

Below are some support articles that can help you in your planning for the upgrade:

                http://support.microsoft.com/kb/946405

                http://support.microsoft.com/kb/942564

                http://support.microsoft.com/kb/944043

                http://support.microsoft.com/kb/977321 -

And you need to make sure that all AD Aware Applications will work fine with Windows 2008/2008 R2 before deploying Windows 2008/208 R2 Domain Controllers.

And please use the below post as your guide for upgrading to Windows 2008/2008 R2 http://technet.microsoft.com/en-us/library/upgrade-domain-controllers-to-windows-server-2008-r2(WS.10).aspx