One of the things I have purchased in the past (and are usually not very cheap) and could be effectively printed by my MakerBot (which I am still waiting for my kit) would be molecular model kits. I quickly made up some common bond configurations and types. I will probably add some more once I actually have a MakerBot to test the prints. I kind of eyeballed the tetrahedral atom so print that at your own risk (as with the rest of it). I am also including the scad files so you can add additional types, change the relative atom sizes (to represent the relative sizes of different elements), bond lengths, and so on.

1. Print the components you want
2. Assemble them and have fun!