PLOTFOODWEB makes it easy to produce nice 3D representations of ecological food webs. The only required argument is the adjacency matrix of predator-prey connections. Sizes, colors and trophic levels can be specified as optional arguments.
Ronald: The data comes from the niche model (Williams & Martinez 2000), with S= 100 and C= 0.15 (if I remember correctly). I didn't save it after generating the figure.