Opale.Soya - High-level, object-oriented 3D engine designed for 3D games in Java. Uses GL4Java to access native OpenGL. [Open Source, LGPL] - http://savannah.nongnu.org/projects/opalesoya/
jPCT - A 3D engine API for Java. [Freeware] - http://www.jpct.net/
Jun for Java - Framework for developing 3D graphics applications. Features include: Geometric elements (point, line, NURBS curve, plane, and surface) and operations (rotation, translation, and resize); Topological elements (vertex, edge, loop, body) and operations (Eul - http://www.sra.co.jp/people/nisinaka/Jun4Java/index_en.html
Anfy 3D - Fast and realistic interactive 3d renderer available for Java. [Freeware] - http://anfyteam.com/panfy3d.html
Imaging the Imagined - 3d animation with Java. 3d graphics come alive with interactive Java programs animating 3D human characters, raytracing creates imagined worlds from mathematical equations. - http://www.frontiernet.net/~imaging/index.html
SyGem Software - Home of Jazz3D, an easy-to-use 3D graphics API for Java. [Commercial] - http://www.sygem.com/