What are the alternative "design methods" to the Model View Controller? MVC seems to be popular (SO was built with it, I know that much) but is it the only method used?
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One of the best write-ups of several different Interactive Application Architecture Patterns out there, is this very detailed and well-researched blog-post. It covers Model-View-Controller, three different flavors of Model-View-Presenter, several different flavors of Presentation-Abstraction-Control, Supervising Controller, Passive View and Hierarchical MVC.
Another interesting pattern is the Presenter First pattern by Atomic Objects. It's not just a Design Pattern, it's also a Process Pattern. IOW: the name "Presenter First" is not arbitrary, it actually describes a development process, in which the Presenter gets written first, driving the design of the rest of the system.
MVC is part of a greater group of design patterns. I have no idea how much experience you have, so I'm not sure how to target this response. I'm a .NET programmer, but I found the Java book Head First Design Patterns extremely helpful. Design patterns are usually broken into groups with other patterns that help solve similar problems.
I also found the Data Object Factory website quite helpful as well. You should look around for some resources in your favorite language.