What happens to stunned flyers?

[SlagMortar]

But no matter how good the maneuverability on the flight you still need to take a action to flap the wings to say up.

Flapping wings to hover in place is not an action. A stunned character is not treated as having 0 Dex, it just loses its Dex bonus. That means it can still defend itself even though it can't take advantage of extraordinary dexterity. A stunned character does not fall prone. A stunned character still makes reflex saves.

A being flying with wings with perfect maneuverablity should continue flapping while stunned and hover in place, in my opinion.

 

[Gerion of Mercadia]

Depends on manuverability class. If you require a move action to maintian flight - you fall. Some creatures have special text. If you don't require an action to maintian flight, you hover or possibly "move with the wind"

 

[TarionzCousin]

The Safewing Emblem (Races of the Wild) is designed for just this sort of occasion. IIRC, it gives you 180' of feather fall when you begin to fall/stop flying.