Most OO 3D games fit quite nicely into the MVC (model view controller) pattern. Check out the patterns book by the game of 4 for more details (or the many websites duplicating their work).
For multiplayer online games a slight addition may be to duplicate the data model between client and server.
Incidently, a good OO design for a 3D game should really apply no matter what API you're using (java3d or JGL)
PS. Just realised, I can get a blatent plug for a UML editor I'm writing in here: http://www.newdawnsoftware.com/jose