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.
Best Answer
Had a similar question come up in a campaign I was running recently. I had to house rule it a no. Immunity isn't voluntary so a ghost cannot go prone just as a Paladin PC with divine health can't voluntarily become infected with lycanthropy. I look at it like the immortal man who wants to die but can't. The mind may try but the physical form can't actually make it happen.