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If GlassFish v3 Gem is installed in NetBeans JRuby installation, then it should be the default option to run any Rails applications. Currently WEBrick is the default and JRuby gem list is not inspected at all.
I added support for the GlassFish Gem to appear as a server. Not sure if it's the default though. Note that the current design of the Gem (specifically the use of the custom glassfish_rails startup script instead of the standard script/server startup) prohibits ruby debugging as implemented in NetBeans from working at all. Best way to resolve that is probably to redesign the gem to use script/server like the others. There may also be less pleasant ways of fixing this.
There won't be any debugging support for Rails apps running on the GEM for 6.5 due to it's architecture so I don't agree with making it the default server for 6.5. Closing as WONTFIX. We can revisit this decision for the next release if there is better support by then (either due to new GEM architecture or support for Debug Attach by the ruby debugger).