TinkerCad is a really fun, simple, and free web-based tool for 3D design. It exports in .STL which goes directly into MakerBot 3D printers.
TinkerCad is very shape based and easy to work with. There are some really useful simple lessons to learn the basic controls. There is also a Thingiverse-like place to explore designs other people have made.
Note: Currently you need Chrome or Firefox to run TinkerCad.
You can also export designs into Minecraft!