Glassfish V2 comes bundled with NetBeans 6.0 Beta versions, and it will be disappointing to find out that it will fail to compile JSPs when you deploy a simple web application. The exception it throws is:
java.lang.NoSuchMethodError: javax.tools.ToolProvider.getSystemJavaCompiler()Ljavax/tools/JavaCompiler
This is solely as Glassfish issue. Calling "java" from the command line shows a Java compiler is available systemwide. Moving the application to an existing SJSAS9 is successful - no such issue is experienced. So, if you have NetBeans 6.0 Beta 2, you should use the Sun Java System Application Server 9.x (separate install) for your Java EE 5 applications. No need to try and troubleshoot. I think a ticket has been logged with Glassfish developers.