The specific example is from a Pathfinder session I was playing in last night. A foe was floating in the air 30' above the ground. I was considering casting Stone Call. The spell has a 40' radius and 20' height cylinder as the area of effect.
I wanted to cast it with a point of origin in the air so the creatures would take the bludgeoning damage (2d6), so at 40' for example. The GM thought that perhaps that would not work because the cylinder must have the bottom on the ground. We didn't really get too far into the discussion because our cleric killed the creatures before it got around to me, but it seems a point that could come up again.
The only description the rules state for cylinder is "When casting a cylinder-shaped spell, you select the spell's point of origin. This point is the center of a horizontal circle, and the spell shoots down from the circle, filling a cylinder. A cylinder-shaped spell ignores any obstructions within its area." This doesn't specifically call out whether that point of origin can be above the spell's listed height or not.
Now this particular spell leaves debris on the ground below it making for difficult terrain for 1 round/level. So there are too basic questions in cases like this:
Can the point of origin be above the spell's listed height?
If so, in spells such as this one, would the ground below still have the debris/difficult terrain since ground level wasn't within the spell's area of effect?
The spell Ice Storm is another good example of this situation.