With clustering now available in GlassFish since version 3.1 (our Spring 2011 release), a good number of folks have been looking at migrating their existing GlassFish 2.x-based clustered environments to a more recent version to take advantage of Java EE 6, our modular design, improved SSH-based provisioning and enhanced HA performance.
The GlassFish documentation set is quite extensive and has a dedicated Upgrade Guide. It obviously lists a number of small changes such as file layout on disk (mostly due to modularity), some option changes (grizzly, shoal), the removal of node agents (using SSH instead), new JPA default provider name, etc...
There is even a migration tool (glassfish/bin/asupgrade) to upgrade existing domains. But really the only thing you need to know is that each module in GlassFish 3 and beyond is responsible for doing its part of the upgrade job which means that the migration is as simple as copying a 2.x domain directory to the domains/ directory and starting the server with asadmin start-domain --upgrade.
Binary-compatible products eligible for such upgrades include Sun Java System Application Server 9.1 Update 2 as well as version 2.1 and 2.1.1 of Sun GlassFish Enterprise Server.
