I was working on some aerial combat rules a few months back, but lost interest in it before I'd gotten the entire thing hashed out. One thing I DID get, though, was the effects of wounds on flying creatures:
A creature with maneuverability of less than Perfect loses flying ability the more damage it takes, unless it has innate flight (like a beholder). For every 25% of its hit points it loses, a creature is reduced by one maneuverability class, to a minimum of Clumsy. This represents blood loss, pain, and damage to vital organs (wings and muscles) that hinders the ability to fly. A creature's fly speed is also reduced by 10 feet per 25% of its hit points it loses, to a minimum of 10 feet per round. Again, this does not apply to elementals or creatures with innate flight ability. A creature reduced to less than 25% of its hit points cannot take any actions besides keeping itself in the air, and even then it can move at only half speed and can't perform any aerial maneuvers; a creature reduced to 10% of its original hit point total cannot fly at all; if is in the air, it immediately starts to fall.
Even if the creature is immediately healed back up to a better hit point bracket (from 50% of hit points to 25%, e.g.), it must spend at least one full round at rest (on the ground, sitting in a tree, etc.), giving its body time to readjust and take the strain off the previously damaged muscles and body parts, before it can regain the higher maneuverability class.
Obviously, damage directly to the wings (for creatures that use wings) inhibits a creature's ability to fly much more effectively and quickly than damage to the creature as a whole. In this case, attacks against the wings that deal damage are considered to be twice as much for purposes of determining a creature's ability to fly.
For example: A griffin with 48 hit points is hit in one wing by another rider's sword, taking 6 points of damage. Since all this damage was to the wing, it counts double – the griffin is treated as being reduced to 25% of its hit points (12 is 25% of 48), and suffers accordingly.
A creature can withstand up to 25% of its total hit points in damage to its wings before they are crippled sufficiently that the creature cannot use them to fly. If only one wing is crippled, it can spiral down to the ground, though it must make a DC 20 Reflex save to avoid crashing and taking 3d6 damage. If both wings are crippled, the creature cannot control its descent and falls straight to the ground.
For example: If the griffin mentioned above took another 6 points of damage to the same wing, it would be crippled; it could spiral down to a safe resting place, but it couldn't take off again until the wing were healed and it had sufficient time to rest and recover.
If you're interested, you can check out the rest of the rules
here. It also covers some combat maneuvers, the effects of weather, and falling rules.