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I registered external Apache Tomcat 6.0.28 server under Services -> Services menu, but it was not visible in Properties -> Run menu in my web project.
The same issue exists in NetBeans 7.2.1
It works for me if I have Java EE 5 project. For Java EE 6 project Tomcat server is not offered. Please, describe exact steps to reproduce.
Works for me as well.