I had myself and my trusted dev friend Surinder stumped on this problem on a recently MS Deployment migration from Windows 2003 (IIS6) to Windos 2008R2 x64.
After tons of google searching and a mixing of a few posts the clue was in the error!
What the problem was that even though the website I moved was .net 2.0 there was a lookup in the web.config:-
‘Could not load file or assembly ‘System.Web.Extensions, Version=188.8.131.52′
I then checked the old server and it had .net 3.5 installed so I installed on the Windows 2008 server by enabling the Feature in Server Manager and voila the website came to life!