You make the difficult terrain affect more than a few feet above ground.
It is known that Underwater Combat's movement counts as difficult terrain (you move at 1/4 or 1/2 speed) if you lack swim speed.
But keep in mind that difficult terrain is not the only way to cause Hampered Movement in combat: Poor visibility and obstacles will also reduce your movement speed.
Windstorm-strong winds can check a creature, which will require a strenght DC 10 (on ground) or Fly DC 20 check (if airborne) to move against the wind. It also cuts visibility by 3/4, which should count as Poor Visibility and thus reduce your movement speed.
Spells with a Spread or Burst range should spread in all directions, including up or down from the point of origin.
The default shape for a burst effect is a sphere, but some burst spells are specifically described as cone-shaped. a burst’s area defines how far from the point of origin the spell’s effect extends.
A spread spell extends out like a burst but can turn corners. You select the point of origin, and the spell spreads out a given distance in all directions.
The finest example of a spell like that is Web:
The entire area of the web is considered difficult terrain.