Bryan,
I personally prefer the JBuilder/Weblogic config. IBM seems to be notoriously behind the J2EE standards. For example, VAJ 4.0 does not support EJB 2.0 specs and will not support EJB 1.1 specs without a patch. Also, I believe that Websphere 4.0 only supports EJB 1.1. In addition to that, VAJ will no longer be supported as Websphere Studio Appication Developer will soon replace it. VAJ does not have a JSP editor (Although it can be used in conjunction with some earlier versions of Websphere Studio). Also, IBM seems to be a bit proprietary (Go figure that).
On the other hand, VAJ has an excellent test environment that enables developers to test their j2ee apps thru VAJ and I like their EMSRV repository for source control. Especially for small development teams.
As far as which is more popular, I believe they are both running neck and neck but both are way ahead of the rest.
It is completely a matter of opinion and I suggest that you download the trial versions of these products and test them for yourself.
Hope this helps.