This week's giveaway is in the EJB and other Java EE Technologies forum. We're giving away four copies of EJB 3 in Action and have Debu Panda, Reza Rahman, Ryan Cuprak, and Michael Remijan on-line! See this thread for details.
Lots of factors. What JVM tuning have you done on your stand-alone to match what JBoss AS has?
There is no added layers, Hibernate is an implementation, so both are running Hibernate code, so they are identical in that regard. So that just leaves the container on the outside that is different. JVM tuning is my first guess.