I do not have the books on hand, and I will assume you are the Games Master of your game in this answer.
Yes, flying creatures can be made "Prone". Even though they are not lying flat on the ground (since there is no ground), you can think in the line of the 3.5 rule:
A flying creature with the status of prone has lost control of flight. If it is not buyoant, it will begin falling to the ground. There is no rule on how fast it falls (if it is some parachute effect from its wings/wirlwind/etc). It can spend a move action to recover control (stop falling and losing the bonuses).
On the buyoant thing, Air elementals, beholders, any levitating monster, djinn and the like can be considered buyoant, even though they are heavier than air. For spells and effects, its a bit trickier, check the specific description. Also, if the creature is not buyoant but do not have a minimum forward speed, it can still fall, but won't fall as fast as a rock.
This creature ALSO changes position involuntarily. Melee opponents will have to spend move in order to keep melee range, BUT they probably can't keep up with the speed of a falling creature unless they are crazy enough to allow themselves to plummet also. I don't have the books here, so I am unsure if it should provoke an AoO.
Ranged attacks still suffer the penalty. The flying creature is flailing around trying to recover control of flight, so its harder to hit.
The prone/falling creature could use a feat or skill to recover the flight faster. If I was a flying character, I would like to regain my standing as a free action.
It is like the pixie in "Dust: an Elysian tail" said:
It is not because I can fly that I am not afraid of heights, you know? I can still fall.
I am unsure what you meant by burrow or teleport. If the creature can teleport while flying? probably yes, but there is the concentration issue. I think that for a falling landlubber (elf wizard had flight dispelled), I would call some sort of check to see if he keeps the cool enough to be able to cast.
Not related to D20 or M&M, but in an Earthdawn campaing, our windling warrior only fought either on the ground or at a height greater than one round's worth of falling. Better safe than with broken bones, I guess.
Finally, for M&M, I would go for what is more dramatic. Yes, you can apply the rules from D20-ish on that system, no problem.
Id love to go in to the physics reasoning as to why this may work, but unfortunately your character is in the DnD world and physics doesn't always apply. The short answer to your question is No (flying a grappled target harder into the ground would not do extra fall damage).
The reasoning is twofold - grappled targets and falling/falling damage.
First moving a grappled target (from PHB pg195):
Moving a Grappled Creature. When you move, you can drag or carry the grappled creature with you, but your speed is halved, unless the creature is two or more sizes smaller than you.
So your speed is probably halved when you are flying with the target. This has nothing to do with difficult terrain.
But more importantly (and even if your speed wasn't halved), at 60ft per move (120ft double move/round, which is 6 sec), you are traveling at 20ft per sec or about 14 miles per hour. When you are falling, falls are instant or at terminal velocity (this is DMs call as we are in the DnD world not earth), but in a nut shell, you fall much faster than you can slam someone. Thus there is an argument for taking less fall damage by flying someone into the ground than if you simply dropped him from that height.
Best Answer
The rules simply didn't take the flying case into account. You'll notice there is no reference in any of the entries in the table to losing a wing instead of an arm. I think it was simply written before these flying races became playable.
The highlighted text makes perfect sense if you are restricted to using your legs to move around but makes no sense if you are flying and wasn't landing at the end of your movement. But, rules as written, it says what it says. I would suggest that a DM that makes you fall prone is taking the rules too literally.