Is there a reference game showcasing jME3?

JME is generally built and it’s difficult to tell if a game is “properly” structured or not. However,if you understand the [Application States] (https://jmonkeyengine.github.io/wiki/jme3/advanced/application_states.html#toolbar) you should be able to make a good hierarchy for your project. You can look for code examples in the page i linked and if you’re looking for a template,check those threads:

[BootMonkey] (Bootmonkey - bootstrap your JME project)
[Android Template] (Bootmonkey - bootstrap your JME project)