Whenever you want to use jruby or rubinius, you'll be forced to use gems that are compatible.
Many gems has been implemented using C extensions and you can not use them along jruby e.g.
Regarding others, mostly they clearly states their thread safety status.
So choosing jruby or rubinius will narrow down your options regarding the gems. but a huge opportunity will be exposed, you'd be able to use many mature Java Libraries(in jruby case).