- Stereoscopic vision - as the first answerer says, the eyes each perceive a slightly different version of the world, and the brain can use this discrepancy to guess at the depths of various objects.
- Overlap - if part of object A appears to be blocked by the shape of object B, object A is probably behind object B. (Consider a man peeking from behind a tree.)
- Tapering - the sides of regular, parallel objects appear to get smaller the further away they are from us, so the brain can use this tapering to infer depth.
- Relative movement - as we move, objects near to us seem to whiz by our visual fields, while objects further away (e.g. mountains) move relatively much less.
- Light and shading - since light tends to come principally from one direction, a three dimensional shape should have its sides shaded differently depending on how much they are facing towards or away from the light.
Hope this helps! If this interests you, I can do no better than to refer you to chapter 4 of "How the Mind Works" by Steven Pinker.