What are the different architectures for developing professional and organized Java Web Applications? I have heard about MVC architecture, what architecture else does, for example, Stackoverflow, google, orkut, etc.. use for a scalable, robust and easily-maintainable-from-the-developers-point-of-view, exist!
Quite honestly, most "web applications" are probably written in PHP.
Anyway read up on web frameworks, but to get you started here is a list of the most widely used web framework (that I can think of).
Ruby : Rails
Python : Django
Java : Spring
C# : ASP.NET MVC
Then there are specialized things like Google Web Toolkit
for writing Gmail like apps.
Personally I lean towards ASP.NET MVC and Django, but Rails and Spring are pretty good as well.
But there is a LOT more than just the web framework for many of these applications. Lots of AJAX, Javascript, Flash, scripting, etc. etc.
But definitely start using one of the above 4 (or 5 if you need GWT).
Personally I like Spring MVC for both small or big things. Using frameworks takes a lot of the hassle out when creating a java web app.
Apache Struts used to be (years ago) very popular and the few times I wrote some sort of small web framework it always resembled the Struts patterns for some reason. So it could be a good idea to look at some of these frameworks first and if you later on still want to create your own keep the framework you liked the most in mind.