The answer to your questions depends on your project requirements. If you don't require the Java EE features like message queues, container managed global transactions etc then go with tomcat+spring.
Also from experience I have found that projects that require a lot of web service integration, scheduling, message queues are best best done using some of the Java EE stack.
The good thing is using spring you can still integrate with Java EE modules running in an application server.
Java EE 6 is very different from the previous releases, and it really makes everything lot easier. Java EE 6 combines the best ideas from the diverse Java community - for instance Rod Johnson from Spring framework was actively involved in the making of the Dependency Injection JSR in Java EE 6. A benefit of using Java EE 6 is that you are coding according to a standard, which could be important in some organizations for vendor support etc.
GlassFish v3 supports Java EE 6 and it is quite light-weight and starts up really fast. I have been using glassfish v3 for my developments, and it is really easy to configure. It comes with a very user-friendly admin console that lets you graphically administer your server.
If you are using GlassfishV3 and JSF 2, then you can take advantage of the CDI features of Java EE 6, that lets you easily create conversations (e.g. wizard like pages) in JSF.
Having said that, using Java EE 6 also requires you to learn a new API. Depending on the timeframe available it might not be the best choice for you. Tomcat has been around for ages, and the tomcat+spring combination has been adopted by many web projects, which means lots of documentation/forums are around.
