The way we do it at my present company is to make sure CommonControlsWebApp
is a WebApplication, not a web site. Then you use names for the folders that would help identify it as the common ones that are distinct from the individual web apps. (CommonUserControls instead of just UserControls)
In your other web apps, you create a virtual directory to the CommonUserControls, etc, and add a file based reference to the CommonControlsWebApp.dll
This requires you to use IIS for development (not casini), and Visual Studio won't believe that the controls really exist, but it will work at runtime, and you can build just fine with only warnings about blahblah.ascx or blahblah.master path invalid.
If you do use common master pages and Visual Studio 2008, you will need SP1 for 2008 and use a __fallback.master in the root of the individual web projects to go in to design mode.
However, I saw this on another thread, and I am going to look into doing more like this:
http://webproject.scottgu.com/CSharp/UserControls/UserControls.aspx