I recently came across one of those annoying deployment issues when I deployed my WCF project to a windows 2008 R2 server.
After much googling and scratching my head till I could feel my scalp going raw, I figured out that WCF activation needs to be added as a feature through the Server Manager.
When I actually figured that part out I was caught on a another mind-boggling experience. .Net framework 4 was not available via the Server Manager. But I look at the WINDOWS\Microsoft.NET\Framework folder and there was .Net 4.
Anyhow I figured this out too, you need to have the Microsoft .NET Framework 4 (Standalone Installer) for Server Core
So things to watch out for
1) .Net 4 (Server Core) edition is installed on the windows 2008 server
2) Make sure that you add the feature WCF Activation is added to the server.