I had the same problem (NetBeans 6.8, Glassfish v3, JSE 6, JEE 6).
According to information found on the Web, I included in the project libraries javaee.jar and appserv-rt.jar from the Glassfish lib directory. The client connects to Glassfish from NetBeans but not outside it (class not found com.sun.enterprise.naming.serialInitContextFactory).
This class is supposed to exists in the appserv-rt.jar library. However, the latest version of this library are empty, containing just int he manifest file indirection to the libraries (.jar) located in the "lib/module" directory of the Glassfish installation. It seems that the indirection works when run from NetBeans but not outside.
In order to have it working, I added to the project libraries the two .jar files from Glassfish "lib" directory plus all the .jar files from Glassfish "lib/module" directory. And it worked !
I tried also to locate the missing classes and to add the libraries one by one, but I got some injection and linking errors I could not solve.
Maybe someone knows the minimum necessary set of libraries to add?
Hope it helps
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