The clouds were rendered in two steps. The texture itself was created by rendering volumetric clouds in Blender. The display in the game itself is done through screen-width quad fills whose texture scaling and offset is adjust based on the plane position and the distance to the cloud.
The clouds, boxes & plane were also modelled in Blender and rendered to sprite sheets. The plane animation is a combination of an up-down rotation from the sprite sheet and a simple left-right rotation for the banking. The smoke was implemented through a starling particle system, designed with Particle Designer.