jMonkeyEngine
The longest-lived 3D game engine for Java — open, BSD-licensed, and proof that you can in fact write 3D games with a garbage collector.
Mark Powell started the project in 2003, when 3D in Java mostly meant applets and Java3D. jMonkeyEngine offered a scene graph, shader-based materials, physics and audio on top of OpenGL, and was rewritten from scratch as jME3, with 3.0 going stable in 2014. It runs anywhere there is a JVM, Android included.
It never had a breakout hit on the scale of Minecraft, which was written without an engine at all, but it keeps a loyal following of indie developers and turns up in simulation and teaching. Compare it with libGDX and the difference is clear: libGDX is a framework you build on, jME an engine you build in.