Often overlooked is the decision about which J2EE application server to use. Because a number of the most popular application servers have a significant cost to them, the price of the application server can be a limiting factor. My personal choice in most situations is the open source application server JBoss. Not only is it a very robust server but being able to look at the source code when you have a very obscure problem can also be invaluable.
Whichever server your team ultimately decides to use, a thorough review of the positives and negatives of each server should be considered. Connectivity to existing applications that are in place and the existence of a currently running application server in the same environment can be significant factors. It is generally a bad choice to inject multiple application servers into a single company or set of projects. The additional overhead almost always cancels out any perceived benefit.