I just spend a little to long getting a Windows Communication Foundation service working with Sitecore. It should be straight forward (and I guess it used to be!?). I followed the instructions from this blog post on configuring Sitecore to host WCF services.
This would suffice on Sitecore installations up to version 6.4.1 Update-4. From that version onwards Sitecore introduced a RewriteModule that does not like the URL format of WCF service methods (i.e. ServiceName.svc/MethodName). Sitecore released a fix for this a couple of months ago. The issue notes only mentions ASP.Net web services, but is essentially the same problem experienced with WCF.
Hope this will save you some time and head scratching. I suggested that Sitecore support puts a mention of WCF on the issue notes.