Single Application Code deployment for multiple web sites

Question

At present we're hosting an application called RenderServer which is deploy on server for individual client. It has its own web.config file for all the settings, and the application code for a specific user. In case of Shared hosting where multiple RenderServer would be running on same machine for different clients, we have to deploy all the Code files individually for everyone which is a bit hassle in terms of deployment. So Ideally we are looking to have Single Application Code deployment (I mean single virtual directly folder) for all web sites to share the same code. Please give your suggestions whether it's possible or not and if possible then what are possible ways.