When I install ASP.NET MVC 3 RTM on Windows Server 2008 R2 (Web server edition) will I also be able to run MVC 2 and MVC 1 web applications without installing them or do I need to install all of them separately?
You would need to install all 3 separately. If you want to avoid installing them altogether, you could bin deploy your applications. It's easy.
For mvc 1 and 2: http://haacked.com/archive/2008/11/03/bin-deploy-aspnetmvc.aspx