I dont have a formalized view of considerations as such but can list some factors in making the decision:
Redeployment - Frequent redeployment causes problems in EARs with memory fragmentation so how often will we need to be releasing updates. Will these need an outage on the servers (if deployed on JBoss/Weblogic)?
Shared Resources - Access to shared resources such as JDBC etc if bundled in the same EAR. Will these cause contention and can I make changes to one without affecting the other? Usually all WARs will get affected by changes made at the EAR level.
Upgrades to servers - Deploying with Tomcat and so on requires a possible upgrade to the base web container to take advantage of new Java/server features when available. Example Tomcat 6 to 7.
Size - Downloadable size of installation package if distributing container along with application. How large should we keep it?
Control over configuration - Internal config within my app plus access to config.xml or server.xml on the underlying containers. Do we want clients to edit these? or do we bundle all these in with preferred settings?
Memory footprint - Full blown servers obviously need more Heap (Xmx) than a Winstone app
What is client already running - Existing servers in their data centre could be re-used if Weblogic or Tomcat infrastructure already in place (for example).
Cluster requirements - will an additional performance requirement require adding servers into a cluster? How good is JBoss clustering versus running on Tomcat and what is the impact on the application code in clustered environment w.r.t. caching etc ?