We use Qubicle for all the voxel art. Stonehearth consumes .qb files natively and our resource file format is just JSON, so it's really easy to get new art assets into the game. We used 3DSMax for rigging and animation (later we switched to Maya), but the animation file format is, again, just JSON. The 2D art are .png files, created with Photoshop.
It's easy to create mods for Stonehearth using only JSON, and there's a variety of free tools for creating the 2D / 3D art.