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Bleh, this article made me want to hurl. While Java EE developers are debating the definition of 'application server', developers using other platforms are building applications (and 'enterprise'-worthy applications at that)!
Yes, the author spent way too much time before getting to his relatively trivial point:

Where Tomcat and other Web servers fall short is in the area of features such as distributed transactions, EJBs, and JMS. Applications requiring support for these components are usually more at home in with a Java EE application server such as JBoss, Geronimo, WebLogic, WebSphere, or Glassfish. Many Java EE application servers actually use Tomcat as their Web container.

This is what's wrong with Java:

J2SE, J2EE, EJB, JDNI, JMS, JTA, WAR, JAR, ERP, DAO, EIS, JSP, JDBC, XML, HTML, EAR, JAAS, JAF, JPA, JMX, JAXP, JAX-RPC, JAXB, SAAJ, JCA, SOA

Every single one of those acronyms (and probably more) were used in that article.

And, if you read this http://discuss.joelonsoftware.com/default.asp?joel.3.219431.... and thought he was exaggerating, think again. This is what I had to do to parse an XML file in Java the other day:

    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder builder = factory.newDocumentBuilder();
    Document doc = builder.parse(new File("something.xml"));
    Element root = doc.getDocumentElement();
Sigh