What is the main difference between a Rapid Application Development tool like MonoDev and Visual Studio, is an RAD more focused on one thing? I'm looking to make a web application, are there advantages to using a Web Based Rapid Application Development Tool as opposed to Visual Studio with the .NET framework 3.5 support?
Both are RAD tools. The main difference is Visual Studio is created by Microsoft and, in many ways, has more bells and whistles. Technically, you can use it for mono, but if you want to target both Linux (etc) and Windows with Mono, you may find MonoDev an easier ride. It really depends on what you are doing. At minimum, you will have some re-referencing if you move .NET code to mono.