Standalone server build should be a different target like Android, iOS. When you build it now, it includes server side code to the client. it will cause security issue. there should be platform defines for server code. (http://docs.unity3d.com/Manual/PlatformDependentCompilation.html) Separate platform target can eliminates some graphics/shaders that will not run on the server. For each room i have to run separate MyGame.exe. my simple test game consumes 100MB RAM on the server....
Standalone server build
Standalone server build