I was able to get this working with JBuilder X Developer. It's kind of ugly, you have to work-around all the JBuilder library features.
I did the following. You'll need to update your paths appropriately.
Install Tomcat 5 to a directory (C:\jakarta-tomcat-5.0).
Create a new configuration based on "Application".
Set the Main Class to org.apache.catalina.startup.Bootstrap
Set the VM parameters to be -Dcatalina.home="C:\jakarta-tomcat-5.0" -classpath "W:\common\jre\lib\tools.jar;C:\jakarta-tomcat-5.0\bin\bootstrap.jar;ALLYOURCLASSES;"
Set the Application Parameters to be -config "J:\javadev\Tomcat\conf\server8080.xml" -nonaming start
On the Library tab, set it to only use specified libraries, and then remove all the libraries.
The key thing you'll need to do is figure out the classpath that would have been used if all the libraries you needed were included. For the classpath string in step #4 above, I actually have really long string that lists all the JDBC drivers and libraries we use.