Unity3d is a free program that allows you to make simple objects and terrain. A lot of people use it, and you can program in C#, JavaScript, and other languages. I personally like the Unreal Engine. For doing complicated things, you'd need to learn UnrealScript, but for many things you can use their very easy visual scripting. It used to be called Kismet, though I think it's changed its name. I like Unreal better than Unity 3D just because the modeling is much easier, and the terrain features are very nice. I also like animating in it. You can make a great looking prototype a lot faster, I think. But if you intend to use a separate 3D modeling program, I hear good things about Blender, though I've never used it. All of these tools are free, by the way :)