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Selecting JBoss as a deployment target on a new web project disabled the Java EE5 option, leaving only J2EE 1.4. Since JBoss allows development of EJB 3.0 apps (their entire web framework Seam is based on EJB 3.0) the Java EE5 option should be enabled when JBoss is selected. Right now it only allows Glassfish/Sun Application Server.
Just to clarify: this works properly if creating a new Enterprise application. In that wizard, selecting Java EE5 shows both JBoss and Sun App Server in the dropdown. However, in the new Web application wizard, when selecting JBoss the Java EE5 option is removed from the dropdown, so there is a discrepancy between the two wizards.
JBoss 4.0.4 does not support Java EE 5 based web applications. It supports Java EE 5 only in EJB module and there such option is enabled (Java EE 5 option is enabled only where it does make sense/is supported by the server itself). Therefore marking this as invalid.