Trinidad gem / Embedded Tomcat
If you dig deeper into the Trinidad gem page on Github there are links to the various Trinidad extension gems. There is a daemonizing gem specifically supplied for use in production here:
http://github.com/calavera/trinidad_daemon
If you execute the install script and answer a handful of simple questions, it generates a tailored init script for your Ubuntu or OS X machine. That's pretty much all you need.
There are also example init scripts in the wiki here:
http://github.com/calavera/trinidad_daemon_extension/wiki/init.d-scripts
Note that for use in the Rails.threadsafe! mode, both min and max JRuby runtimes are set to 1 in your trinidad.yml configuration file.
I have it working on Ubuntu with an Nginx frontend, and it's working very nicely.
So yes, this means that you use the command line to stop and start the application server, but the init script will also be called automatically on system startup. The wiki also includes some Capistrano deploy script examples, so you can even have the server stop and start from your own machine.
Note: There are two daemon extensions. The one I have linked to is the new one, which uses a better daemonizing library.
GlassFish gem
You're right, the GlassFish gem isn't getting so much love right now, but I daresay things will improve. There are a couple of issues running it with JRuby 1.5+ because the gem didn't keep up with changes in JRuby, however I wrote about how to work around the issues here: http://www.scottlowe.eu/deploying-rails-3-with-jruby-daemonized-glass
Since writing that GlassFish post, Trinidad has gained the power to be dependably daemonized, so it's probably the smoother path to take today.