Here is an application that I wrote that will allow you to select a running application and keep the windows running on top of all of the other applications. This has been tested on Windows XP/2003/7. I assume that it will work on Vista. There isn’t an installer just download the executable and run the application. The application was written in AutoIT and I have included the source code. It is release under the GPL v3 license.
Application: RunOnTop.exe (142)
Source: RunOnTop.exe Source (162)
Screen Shot of RunOnTop.exe