After installing .NET 3.5 on a portion of our dev and test environment we found that things were suddenly broken. We have a significant portion of "old" WCF (.NET 3.0) apps that were hosted in IIS (yet another good reason to self host - insulation from lousy installers). After looking into it a bit (and an unsuccessful Google of it) I found that it removed the .svc extension handlers in IIS. Good great and wonderful if you're running 3.5 perhaps, not so much if you still have to support 3.0.
UPDATE: As it turns out, this was due to faulty installation of 3.5 which yieleded a MSVC++ error during installation. A successful installation will not remove the extension handlers, however when you click to proceed, it informs you that the installation was successful. Un-installing, then re-installing 3.5 did the trick.