Visual Studio 2012 has a pretty good code coverage tool. I have used it to measure code coverage of a web service.
It is easy to integrate into build systems, you have out of the box support for TeamBuild (the TFS build) - see a more detailed article here.
According to msdn it has result merging.
Code coverage is also integrated in Microsoft Test Manager, so you can have manual testers do a round of testing on your service and at the end see how much of the code they actually hit.