<p>We have a product but we are doing some rebranding so we need to be able to build and maintain two versions.  I used resource files combined with some #if stuff to solve the strings, images, and whatever else, but the program icon is giving me trouble.  I couldn't figure it out from msdn or a google search.  Thanks!</p>

Set the icon in normal code, and you should be able to use the same techniques as you have elsewhere. You'll need both icons in the resources file (at least so I suspect) but it should work.
Alternatively, set a prebuild step to copy the appropriate icon into a common filename - e.g. copying debug.ico or release.ico into app.ico. A bit hacky, but I think it would work. That way you only end up with one icon in the finished binaries.
Yet another option: look into the build file and see how the icon is built in, then conditionalise it. Marc Gravell did this for references in
MiscUtil
- the project can be built targeting either .NET 2.0 or 3.5, depending on configuration. I suspect that resources could be conditionalised in a very similar way.