The description of a cylindrical area of effect is
A cylinder’s point of origin is the center of a circle of a particular radius, as given in the spell description. The circle must either be on the ground or at the height of the spell effect.
This seems to indicate that the cylinder is always touching the ground, and is consistent with some chat comments I've had. So, for example, consider you have a 50ft high cylindrical spell. You either cast the point of origin on the ground and it grows 50ft up, or cast it 50ft up and it descends 50ft.
That being said... What if you're on top of something?
Is the height at which you cast the spell based on the height at which you are when you cast it (and so, if you're on top of an expertly drawn tower, can you hit enemies above you, but way above the spell' range from the ground) or is the height always in relation to the ground (meaning it doesn't matter where you are, but only where you cast it)?