This post visualizes changes between Java EE Standards 5 and 6. The comparison of standards is listed in four sections Web-Services, Web-Container, Enterprise Application technologies and Maintenance. Hope this helps someone.

Web Service related changes

JAVA EE 5 (JSR-244)	JAVA EE 6 (JSR-316)
JAX-RPC 1.1 JSR 101	JAX-RPC 1.1
Enterprise Web Services 1.2 JSR 109	Enterprise Web Services 1.3 (new version)
Web Service Metadata 1.0 JSR 181	Web Service Metadata 1.0
Streaming API for XML 1.0 JSR 173	Streaming API for XML 1.0
JAX-WS 2.0  JSR 224	JAX-WS 2.2 (new version)
JAXB 2.0 JSR 222	JAXB 2.2 (new version)
SOAP with Attachments API for Java (SAAJ)JSR 67	Java APIs for XML Messaging 1.3 (new version)spec
	new! JAX-RS 1.1 JSR 311
	new! Java API for XML Registries (JAXR 1.0)JSR 93

The new redesigned Java API for XML Web Services (JAX-WS) is the base or a middle part of a newly Java EE 6 Web service stack.  The new stack  includes JAX-WS 2.0, JAXB 2.0, and SAAJ 1.3. and is also called “integrated stack”.  JAX-WS was designed to take place of JAX-RPC. Due this also JSR-109 was updated because it describes run time architecture of JEE Web Services Stack. JAXB which provides an easy way to bind an XML schema to java and vice verse, was updated to.

The SOAP with Attachments API for Java (SAAJ) (also known as Java APIs for XML Messaging (JAXM)) provides a standard way to send XML documents over the Internet from the Java platform and was updated slightly containing now other consolidated standard.

New are JAX-RS, which provides support for RESTful Web services and JAXR which enables pull-parsing API for reading and writing XML documents. Also available in Java SE.

Web Applications related changes

JAVA EE 5	JAVA EE 6
JSTL JSR 52	JSTL
JavaServer Faces 1.2 JSR 252	JavaServer Faces 2.0 (new version)
JavaServer Pages 2.1 JSR 245	JavaServer Pages 2.2 /EL 2.2 (new version)
Java Servlet 2.5 JSR 154	Java Servlet 3.0 JSR 315 (new version)
	new! Debugging Support for Other Languages 1.0 JSR 45

In Java EE 6 we have updates of all technologies of the Web Container except JSTL. So e.g. Servlet 3.0 improves Servlet concept in pluggability and some ease of development. It’s also introduces Async Servlet, and long waited File Uploading!. Also now configuration can be done by annotations.

New a specification of Debugging Support for Other Languages 1.0
This describes standardized tools for correlating Java virtual machine byte code to source code of languages other than the Java programming language, so it would guarantee debugging possibility of everything what runs is JSR-45 certified container.

Enterprise Technologies changes

JAVA EE 5	JAVA EE 6
Common Annotations JSR 250	Common Annotations
JCA 1.5 JSR 112	JCA 1.6 JSR 322 (new version)
JavaMail 1.4	JavaMail 1.4
JMS 1.1 JSR 914	JMS 1.1
JTA 1.1 JSR 907	JTA 1.1
Enterprise JavaBeans 3.0 JSR 220	Enterprise JavaBeans 3.1 JSR 318 (new version)
JPA 1.0 JSR 220 (together with EJB 3.0)	JPA 2.0 JSR 317 (new version)
	new! Contexts and Dependency Injection for Java (Web Beans 1.0) JSR 299
	new! Dependency Injection for Java 1.0 JSR 330
	new! Bean Validation 1.0 JSR 303
	new! Managed Beans 1.0 JSR-316

In Enterprise Application section we see some important changes and new specifications. Most famous and important is  JSR-299 Context and Dependency Injection (CDI) which is there to unify the JavaServer Faces-managed bean component model with the Enterprise JavaBeans component model to simplify the programming model and architecture of web-based applications. Look an Weld Framework as reference implementation to this.

The similar sounding Standard Dependency Injection for Java JSR-330 just define a standard and common known DI like in spring and other frameworks. Look at popular Guice DI-Framework from Google which implements JSR-330.

Bean Validation  introduces a very cool annotation based and architecture layer independent Java Bean validation.

There are also some interesting improvements in EJBs. Singleton is a new type and can be only one per container, it is also possible to use @Local Beans (Same VM) without interface. Also JPA 2.0 has advanced query possibilities and validation.

Management Technologies

JAVA EE 5	JAVA EE 6
J2EE Application Deployment 1.2 JSR 88	J2EE Application Deployment 1.2
JavaBeans Activation Framework (JAF) 1.1 JSR 925	JavaBeans Activation Framework (JAF) 1.1
J2EE Management 1.0  JSR 77	J2EE Management 1.1 (new version)
Java Authorization Contract for Containers 1.1 JSR 115	Java Authorization Contract for Containers 1.3(new version)
	new! Java Authentication Service Provider Interface for Containers JSR 196
	new! [JavaSE] JAXP 1.3 JSR 206
	new! [JavaSE] JDBC 4.0 JSR 221
	new! [JavaSE] JMX 2.0 JSR 255

Nothing special to mention here.