If a flying creature takes falling damage from the fall due to being knocked prone, it is prone on the ground, otherwise it lands safely.
Prone:
When a creature is prone, it is lying down. If the creature is climbing or flying when it is knocked prone, it falls instead.
Therefore, flying creatures fall.
Flying:
Falling Prone: If a creature falls prone while it is flying, it falls. This means a flying creature falls when it becomes unconscious or suffers any other effect that knocks it prone. The creature isn’t actually prone until it lands and takes falling damage.
Therefore, a flying creature may or may not be prone, depending if it takes damage.
Crashing:
Falling while Flying: If a creature falls while it is flying, it descends the full distance of the fall but is likely to take less damage than a creature that can’t fly. Subtract the creature’s fly speed (in feet) from the distance of the fall, then figure out falling damage. If the difference is 0 or less, the creature lands without taking damage from the fall. For example, if a red dragon falls when it is 40 feet in the air, subtract its fly speed of 8 (8 squares = 40 feet) from its altitude. The difference is 0, so the dragon lands safely and is not prone.
If a creature is flying when it starts a high-altitude fall, it has one chance to halt the fall by making a DC 30 Athletics check as an immediate reaction, with a bonus to the check equal to the creature’s fly speed. On a success, the creature falls 100 feet and then stops falling. On a failure, the creature falls as normal.
Therefore, if a flying creature is knocked prone at a distance of more than its fly speed, it takes damage and is knocked prone at the end of its fall. If a flying creature is knocked prone at a distance of less than its fly speed, it is merely grounded until it can take off again (provoking attacks of opportunity as appropriate.)
As a curious note, inflicting the "slowed" condition on a flying creature before knocking them prone is an excellent way of causing them both falling damage and being prone at the end of the fall, as the slowed condition reduces their speed.
The only movement allowed a prone creature is crawling, teleportation, or forced movement:
A prone creature takes a -2 penalty to attack rolls, and the only way it can move is by crawling, teleporting, or being pulled, pushed, or slid.
Therefore, a prone creature cannot fly.
Hover may prevent a creature from falling prone, but only from inference
Fly Speed:
A creature that has a fly speed can fly a number of squares up to that speed as a move action. If the creature is stunned or knocked prone while flying, it falls. See also hover.
Hover:
If a creature can hover, it can remain in the air if it is stunned. See also fly speed.
There is an argument to be made that knocked prone is countered by hover due to hover also countering stunned. It is not present in the rules however.
A creature hovering or flying one square off the ground with a fly speed of more than 1 lands safely when knocked prone, and therefore does not take falling damage. The lack of falling damage means that the creature is then not prone.
A creature flying at ground level is still in the "flying" mode of operation. and there are no minimum altitude rules. It can be assumed that a creature with hover will be flying at all times, and a creature with flight but without hover will be flying whenever there is little chance of being stunned or when its fly speed is greater than its ground speed.
No, standing from prone doesn't trigger booming blade's damage.
I don't see any specific rules definitions for "movement." Based on definitions in other editions, my opinion is that a character "moves" when they walk or use some other "special type of movement" such as jumping, flight, swimming, etc: when they move from their original position, rather than just standing up, dismounting, or otherwise reconfiguring their posture but remaining in the same place.
The spell doesn't say "if the target willingly takes any action." Therefore, attacks and environment interactions are probably fine. The spell doesn't force you to remain perfectly stationary like a statue. Given this, it seems clear to me that doing things that use movement but don't change your tactical position don't count.
Some places in PHB190-191 use the phrase "deduct... from your speed" instead of "spending [X] feet of movement." This might be a clearer way of looking at it. Some actions, such as standing up, reduce the amount you can move in the turn even though they are not "movement" for the purposes of triggering spell behavior.
For a useful corollary, it makes sense that mounted movement would still trigger the effect, even though you're not using your own movement or deducting from your speed.
Although it doesn't affect the lack of definition in 5e's rules as written, D&D 4e says "Whenever a creature, an object, or an effect leaves a square to enter another, it is moving." 4e rules don't apply to 5e, but they provide insight into the background of D&D rule design.
Best Answer
It's up to the DM.
Both booming blade and this issue are going to come down to a DM call as it is not made explicit or clear in the rules.
To me, "a stunned creature ... can't move" seems pretty clear. The difference between this use of "move" and its use in booming blade1 seems clear to me, but it is admittedly not explicit, and may be seen another way by another DM.
I would rule that you cannot stand up from prone while stunned or paralyzed. This is how I've ruled it before and met no objection from my players, even the one who tried to test it out - likely because the ruling is completely intuitive.
We can find some guidance from the grappled condition:
Notice, when you are grappled, your speed is 0, so you cannot "move" in the sense that you cannot change your position relative to other creatures. But you are still able to move your body. It seems natural to me that this is a weaker condition than "you are unable to move". Stating "a creature can't move" includes "your speed is 0", but is a stronger condition, that further restricts any movement at all; and since this means you speed is 0, we cite the rules for being prone:
Again, the implicit nature of all of this means it is a DM ruling, but this ruling seems quite natural and most supported.
1 "If the target willingly moves before then" quite naturally seems to be talking about changing position on the battlefield.