It really depends what you're deploying. Presumably, you're using .NET or SQL Server, or you'd not be using Windows. In my experience making everything run in

It really depends what you're deploying. Presumably, you're using .NET or SQL Server, or you'd not be using Windows. In my experience making everything run in IIS (with activation, if needed) and using msdeploy to deploy to IIS and SQL Server was the best setup.