I have to admit that I do not have an answer.
Why do I even care? Because I am a Java developer. Like many Java developers, I get along with Java well. Not only the language itself, but the development environments (Eclipse for example), step-by-step debugging helper, wide availability of libraries and code snippets, and the readily accessible information on almost any technical question I may have on Java via Google. Last but not least, I go to JavaOne and see 10,000 people that talk and walk just like me.
The other reason that I ponder this question is that the power of Java is a perfect fit for the areas where websites may need more than markups or scripting, such as middleware logic. PHP and Ruby etc are cool for building pages, but they are not ideal candidates for building middleware logic. Given that Java covers the "high end" of the spectrum well (where sophisticated processing is needed), wouldn't it be great to use Java all the way?
Is it Java as a programming language too difficult to use, comparing with those scripting oriented interpreted languages? Yes, this maybe the reason. But there are 5 million Java developers out there already, and millions of developers make a living by write server side Java code. A lot of websites are built by these Java developers, and somehow they choose to use PHP or Ruby instead. Why? It is even more puzzling that I have seen quite a few Enterprise Java people decided against Java - when they decided to build their web 2.0 site, they went for PHP even though they have to learn PHP.
Is it the lack of tooling? I think there are more tools for Java than, say, Ruby.
Is it the lack of frameworks? I bet there are more Java frameworks than the population in China.
OK, a lot of websites are fairly simple, mainly composed of markup pages, scripts and some lightweight logic on the server side, where PHP and Ruby are good for. Java maybe an overkill for such websites. But there are a lot of websites that are much more sophisticated than "lightweight" logic on the server side. For example, FaceBook was relatively simple initially, but now with FaceBook API and Platform, its complexity is growing. Why not use Java for such websites?
So what is missing from the Java world? What is the ideal architecture to build a website using Java?
- Option 1: JSP/Servlet with a Java Servlet engine (or even an application server): This is the dominant architecture for Enterprise web applications. But it clearly has not been appealing for building websites in comparison to PHP or Ruby;
- Option 2: JavaServer Faces: JSF is the new kid on the block. Is it going to make building websites easier? Probably not. It is designed for simplifying building form-based applications.
- Option 3: Using a Java based content management system (CMS)? I have come across many CMS systems over the last few years, and haven't been impressed by anyone of them.

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