I'm a programmer and would like to help my son learn to program a 3D game in Python that can run slowly on the RasPi or quickly on a PC. I thought about using the RasPi edition of Minecraft, but it looks like that will only work on the RasPi. Are there any other simple options?
I don't recommend starting him with 3D gaming. It's difficult and requires a lot of advanced math. A lot of 2d applications and programs are probably going to be more his speed, other than that...
Have you considered experimenting with blender? It's open source so if it doesn't have a RPi version you could compile it yourself and it has support for Python integration. It's not gameplay per say, but it could do that into mix of scripting and 3d visualization.
You can build a 3d model (some are actually pro quality work) and then animate it using python.