I have been looking for a reasonable high level 3D library for Java for some time. Recently I have been using JME 3.0 (www.jmonkeyengine.org) and it seems to be doing the trick. Here are a couple of pics, one from an accessibility model of Cambridge, UK and one from an on-the-fly pedestrian simulation.
The accessibility model has been produced by a simple tool that takes the a shapefile (.shp) or other GIS polygon file and extrudes it polygon based on one of its attributes. The colour of each resulting prism may represent the same or a different attribute.
This second one is from a thin 3D viewer sitting on top of a pedestrian simulation suite. The 3D viewer receives information about the position, speed and direction of each pedestrian from the pedestrian simulation and updates the positions and kinematics of the skeletons accordingly. The colour of each avatar may represent any of the metrics associated with their motion (e.g. speed, estimated distance to destination, local density, delay etc.).