Back in January, I had a problem adding the Ajax Control Toolkit to my Toolbox with Visual Studio 2008.  The Ajax Controls where grayed out after executing a show all (right mouse click inside Toolbox, select Show All).  My solution: I unplugged my Microsoft Wireless mouse.  After unplugging my mouse, the Ajax Controls appeared.  For more information, follow this link, which contains a posting of my solutiion.

I also did some follow-up research, another possible fix is to make sure your solution is pointing to the 3.5 .Net framework.