I'm using NB 6.1 under Sun's JDK 1.6.0_02 on Windows XP, with both WAS 6.0 and WAS 6.1 defined in the Servers manager.

If I edit the properties of a J2EE 1.4 web application, I can select the Websphere servers as the target server.
However, if I open one of my existing J2EE 1.3 web apps (or create a new one) the Websphere servers are not included in
the dropdown list of available targets.  Since the J2EE spec mandates backward compatibility with the earlier version,
it is perfectly valid to deploy the 1.3 app on these WAS versions, and indeed I can do so manually via WAS' admin
console without any problem.  Certainly other servers that conform to the later J2EE versions are still listed e.g.
Tomcat 5.5 (J2EE 1.4) and 6.0 (J2EE 5).

This was doubly irritating for me since the 1.3 application uses a mail session resource, but Tomcat doesn't include the
javamail & activation libraries so I get a bunch of compilation errors; the Websphere j2ee.jar includes those APIs, but
Netbeans won't let me target it :-(

Conversely, when creating a new web application, if I select Tomcat 5.5 as the server I can choose between J2EE 1.3 and
1.4, but if I select either of the WAS servers I only have the option of J2EE 1.4 even though the earlier version is
also supported by the server.