Some factors that affect perception of depth in photos, along with suggestions you can try:
Stereoscopic vision. Use aTake stereoscopic camerapairs. (Clouds photo presented as R/L/R. Use the pair that corresponds with your viewing method.)
Lighting. Presence of shadows and highlights. Use more directed lighting, as opposed to "flat" lighting.
Depth of field with foreground or background objects that are out of focus. Include foreground or background objects.
Overlapping objects. Change the composition to show objects overlapping.
Objects of varying sizes, especially a reference object of known size. Include people in your photo. (In the right-most clouds image, notice how the drawn in person affects the apparent scale of the image.)
Distortion. Images from perfectly corrected rectilinear lenses look "flat". Use a fish-eye lens.
Perspective I. Distance between objects and the camera. Use a wide-angle lens or take multiple images to stitch together.
Perspective II. Converging and diverging lines. Get close to an object and angle the camera along the object.