I had the case where i was trying to find a Good solution for Making an Installation Package for WCF web service, you might know that Visual Studio introduced a solution for this where we were adding a Setup Project to our web Application project and Things gone very well. but latterly they announced they are not going farther in this in Newer versions of VS and its already missing in VS 2012.
the Question is .. What is the alternative ?
The Answer is WIX .. Wix is an old Project implemented by MS Guy and currently Microsoft invest more and more in WIX. i believe its pretty complicated and miss the Support but its real powerful XMLs based project to Make your Installation very stable and Well Organized.
Install WIX from http://wixtoolset.org/ and it will add a new Projects Type to your VS. you can create your Web or Desktop or Windows Service or even web service MSI Package.
I won’t illustrate more farther what can you do with WIX but for my case i did the following steps through WIX XML configuration.
1. I created an IIS AppPool with .net 4.0.
2. I created a Website mapped to the per created AppPool.
3. I Copied the Publishing Artifacts of my WCF web service to the wwwroot and Mapped the last created WebSite to this folder.
4. I created a folder and Gave the Proper Credentials to it.
you can do more with WIX, just think free of the limitations and you will find a workaround somewhere inside WIX.