Application servers are designed to fit into an overall IT and Internet environment. Thus, the first set of considerations has to be interoperability with what exists (or will exist). The degree to which the overall environment is set influences your application server choice: if you must work with existing databases, Web servers, and the like, you simply check off those compatibilities on possible choices.
When an application server is part of a migration from a legacy system, it may be part of a move to different types of programming (like Java) and operations (distributed and off-site--even colocation). In these cases, make certain that the application server choice includes sufficient support from people who know both sides of the issue--the legacy systems and the new ones.
PERFORMANCE AND SCALABILITY
Getting an application server up and running is only part of the task: plan for the application server you need one or two years from now. That means making estimates of performance needs (obviously a range of estimates), and making certain that the solution is scalable within those estimates. (It is usually not necessary to make certain that the solution is infinitely scalable, and that usually adds unnecessarily to the cost.)
Make certain that the licensing allows a test environment to function. And create such a test environment. If you are moving from a legacy system, your IT department is probably used to creating and managing test environments; however, Web-based systems pose bigger testing challenges (if only because if youre not careful, pieces of the system wind up being stored all over the Internet in caches so cutting over from one environment to another is not always an easy task).
If the application server is a transition from a static Web site rather than from a legacy system, your transition may involve training, retraining, or even hiring IT-savvy people to develop, maintain, and manage the application server. Choose an application server that provides good training and support for the type of people who you will need to train. (Excellent training for IT professionals won't help if you're training a Web team.)
Consider an application server that is used in your industry or market. While many products are very broad based, others cater to specific markets, and you may find support better in these cases. (This issue is listed last because it cuts both ways--sometimes your industry can use a shot in the arm and some new ideas.)
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