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 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?
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.
Control over configuration - Internal config within my app plus access to config.xml or server.xml on underlyign containers.
Memory footprint - Full blown servers obviously need more Xmx than a Winstone app
What is client already running - Existing servers could be re-used if tomcat infrastructure already in place (for example)