Is there a way for you to monitor glassfish through JConsole? JConsole will show you how much PermGen space (as well as other spaces) is being used. Using this information can help you tweak your startup parameters.
This page http://java.sun.com/javase/technologies/hotspot/vmoptions.jsp lists a few and I know I've seen more, esp. when it comes to setting permgen sizes.
You might also want to look at how your webapp(s) are allocating things that go into permgen space. Maybe the problem is there rather than in NB/GF combo.
Finally, is it possible for you to upgrade to NB 6.7? I know it's difficult to change your app server for development, esp. if you deploy to that version of the app server in production (I've experience problems there too). But changing the IDE could help too.
I know this is not an "answer", but I hope it helps.