Espresso3D - A high performance real-time 3D game and application engine with OpenGL rendering for the Java. [Free for non-commercial projects] - http://www.espresso3d.com
AgentFX 2 Platform - A OpenGL 3D-engine offering features supported by the latest graphics cards combined with portability options that come with the use of Java. [Commercial] - http://www.agency9.se/products/agentfx/
JGL - A 3D Graphics Library for Java which is similar to OpenGL. [Open Source, LGPL] - http://www.cmlab.csie.ntu.edu.tw/~robin/JavaGL/