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JBoss or Tomcat, maybe TomEE?

First the facts, neither is better. As you already mentioned, Tomcat provides a servlet container that supports the Servlet specification (Tomcat 7 supports Servlet 3.0). JBoss AS, a 'complete' application server supports Java EE 6 (including Servlet 3.0) in its current version.

Tomcat is fairly lightweight and in case you need certain Java EE features beyond the Servlet API, you can easily enhance Tomcat by providing the required libraries as part of your application. For example, if you need JPA features you can include Hibernate or OpenEJB and JPA works nearly out of the box.

How to decide whether to use Tomcat or a full stack Java EE application server:

When starting your project you should have an idea what it requires. If you're in a large enterprise environment JBoss (or any other Java EE server) might be the right choice as it provides built-in support for e.g:

JMS messaging for asynchronous integration
Web Services engine (JAX-WS and/or JAX-RS)
Management capabilities like JMX and a scripted administration interface
Advanced security, e.g. out-of-the-box integration with 3rd party directories
EAR file instead of "only" WAR file support
all the other "great" Java EE features I can't remember :-)
In my opinion Tomcat is a very good fit if it comes to web centric, user facing applications. If backend integration comes into play, a Java EE application server should be (at least) considered. Last but not least, migrating a WAR developed for Tomcat to JBoss should be a 1 day excercise.

Second, you should also take the usage inside your environment into account. In case your organization already runs say 1,000 JBoss instances, you might always go with that regardless of your concrete requirements (consider aspects like cost for operations or upskilling). Of course, this applies vice versa.

I'd certainly look to TomEE since the idea behind is to keep Tomcat bringing all the JavaEE 6 integration missing by default. That's a kind of very good compromise