First of: I'm new at designing graphics and graphical effects. Therefore here are some corner stones.
To create 3D models we will use Blender. Anyone not familiar with this tool (such as myself) will find lots of tutorials on their page. For 2D models Gimp may be useful as well. Gimp however focuses on manipulation of existing images and not the creation of new images.
Existing models and other game-art can be found at OpenGameArt. A great selection of textures can be found at http://www.cgtextures.com/
The cool looking models created with Blender must be imported into Java. The tutorial Using Blender To Create Java3D Models suggests the use of Blend2Java. The HowTo can be found here. At least for starting it may be easier to have the 3D models in blender and only export the needed views as images, which can be used in the game.
Based on this blog entry I figure OpenPatrician differs significantly enough from 'The Patrician'.