http://community.jboss.org/wiki/JBossAS6FAQ written by jaikirian pai maybe help.
The main functional difference is the that JMS was JBossMessaging (5.x) and HornetMQ for 6.x and the new JEE specification.
AFAIK the HornetMQ will bring a better performance (messages are no longer stored within a RDBMS) especially with a (new) RedHat Linux filesystem.
Scott, I'm still working on some documentation that I hope to publish soon. I'll consider your questions above to include especially a matrix of functional comparison between JBoss 5 and 6. As a quick reference (possibly incomplete from what you're fully looking for), is Scott Marlow's blog on AS 6 Memory Improvements. If you have questions, about other features/functionality be sure to let us know either here or add comments to the JIRAs tracking the AS 6 documention here
Thanks Shelly, I was just reading one of your interviews and came across some other documents/references with the help of the other folks that replied to this string along with some folks from work. Anyway, I have taken a shot at putting together a quick very basic functional comparision (see attached), I'd be interested if you and the others agree. Keep in mind this is very high level and limited not to mention I'm just now getting myself familiar with JBoss. I apologize in advance for pasting in the table as I couldn’t figure out how to get the word document attached.
JBoss AS 5.1.0
JBoss EAP 5.0
JBoss EAP 5.1.0
JBoss EAP 6.0.0
Has everything the EAP 5.1.0 version has except the certification and continued support.
WFK – Framework Certification Program
Includes everything from EAP 5.0 plus the items listed below
Includes everything from prior releases plus the items listed below
Major architecture change – MC 2.0 based
Common Criteria Certification (EAL 4+)
Java EE 6 Fully Certified (end of 2011)
HornetQ 2.1 optional JMS provider
Bundling of the Apache CFX as the back end for JBossWS
Fully Java 5 EE Certified
Apache CXF optional WS stack
JBoss Messaging replaced with the ultra-fast-next-generation HornetQ 2.1.2
mod_cluster – smart HTTP load balancer
Performance (Messaging & Transactions)
Infinispan project replaces JBossCache
Availability of RPMs via RHN
Includes full JTS implementation
Certified on Amazon EC2 (post GA)
Scott, I'll be putting together a functional matrix of the community project version comparisons JBoss AS 5.1.0.GA to JBoss AS 6.0.0.Final. For EAP overview, you may want to look at the JBoss Enterprise Application Roadmap presented by Rich Sharples at JBoss World 2010.