Five or six Permanent-ized Invisible Force Walls above the castle, at angles to each other (spell names in italics). Midair collisions would be as deadly as catapult stones.
One such wall, directly above the castle, parallel to the ground, to protect against dropped weapons.
Dome-shaped castles, yes.
Early warning counts!!–Remote observers, away from the castle, in watchtowers. Drums, flags & signal fires to warn of incoming air raids or armies.
For all the talk of wire, I have to point out that significant lengths of wire are pretty much an artifact of modern technology.
And the whole idea of lobbing stones upward at the flying enemy? Limited at best. They will lose significant kinetic energy flying upward. Then they come back down…
No, I think I’m really liking the idea of limiting exterior access and landing spots (severely sloped roofs anyone?) combined with heavy coverage from well protected archers.
You realize that your arrows are going to lose kinetic energy and come right back down too, right?
You’re right about wire being modern, but some decent cord (maybe magically reinforced) would provide a significant obstacle, even if it wouldn’t cut.
If I were defending that castle, I’d be tempted to grease those sloping roofs to make them even more difficult to land on. Then again, if I’m attacking a castle with greased roofs, I’m probably going to try to light those roofs on fire. This could work against either side- hot flaming grease is going to run right off the roof, onto the head of those below if your drainage is good. However, it could, you know, burn down your castle.
Well yes, but they are potentially going to stick into their targets, not just bounce off like stones. They also have a lot less mass, which means a lot less kinetic energy when they come down. Sure, there’s the whole “pointy” thing on the way down, but we just make sure no one’s having a picnic in the courtyard during the battle, eh?
Don’t grease the roofs, just make them naturally slick with nothing to hold onto, along with the severe slope.
I’m curious as to how much these flying creatures can carry. There’s going to be little point if the attackers can drop ten-ton boulders from a thousand feet up.
I was thinking barage ballons, for starters—with, of course, the obvious problems that a) You may not have balloon technology, b) The attackers could shred the balloons, to take down the cables and/or nets strung between them, and c) they could simply fly above the balloons and attack from any gaps from above.
They may come in handy if—like Disney’s Gargoyles—the winged humanoids can’t actually make powered flight, but have to glide, which could limit their ability to climb to altitude for the attack.
Though I see King of Soup technically beat me to the balloon concept…and smudge pots. Filthy bastard. ( 
) Some ancient chemical warfare techniques, such as burning mustard or sulfur, might be handy, too. Assuming you don’t have any sentimental moral qualms.
Depending on the technology you have available, you might try something like a Fire-lance, an early Chinese gunpowder weapon. Kind of like a primitive fougasse/blunderbuss. (The very cool book Gunpowder has some good info on these, pages 13-15.) Supposedly, they could project a six-foot tongue of gunpowder-fueled flame that would burn for five minutes, additionally with bits of shrapnel (such as metal or crockery bits) mixed in with the powder to be spewed out.
Hell, a Punt gun would be good, too…if it’s getting too steampunk-y, maybe you could rig up one powered by springs, or magic, or a big troll mercenary using one like a blowgun, or something.
Or you could buy some sick poultry from a disreputable Kara-tur importer, and try to give ol’ Voltan bird flu. 
Depends on how good their bomb sight technology is. 
considering this is a fantasy rpg type setting, especially if you want some kind of cool rescue, bailout situation would be flying reinforcements of your own, air elementals, giant eagles, djinn, pegasi, various demons, etc.
Spellcasters will also be of immense help via the fact that spells often lack the inaccuracy of weapon fire and even some lower level spells like sleep could be used with devastating effect on a flying critter.
Do you mean, like, could they carry a … coconut?
Man, I’m glad my D&D GM didn’t think of these for his game. He put us in a small province sitting in between two huge armies: one led by a homicidal maniac baron who was pissed off at our group in particular and this town for giving us aid (so we humiliated him by stealing an ancient artifact he was completely unaware of that had been sitting under his castle for centuries, setting the central market on fire, kidnapping his second-in-command, and blowing the front gates sky-high in making our escape. Is that any reason to be a sorehead?). The other was ostensibly an ally of the province who was waiting for an excuse to swoop in an put them under permanent “protection”. I think the GM expected us to either try and negotiate a peace, or flee with our McGuffin to the next stage of our quest.
As thief, I had the best sneak and snoop abilities, so our mage cast invisibility and fly (so I could get to the enemy camp and back before the invisibility wore off) on me so I could check out what we were up against. I found the Baron’s tent and his main strategy center, checked out how many and what kind of troops he had, then buggered off.
We were mulling over what to do when suddenly it hit me:
“Hey, you can cast fly!”
(mage) “Yeah.”
“And you’ve got more fireball spells than you know what to do with.”
“uh… yeah” (this was a sore point with him. The market immolation mentioned above was unintentional)
“Nuke them from orbit!”
We waited until nightfall and managed to fly over the enemy camp undetected. After re-locating the Baron’s tent we unleashed a high-altitude bombing campaign (in addition to the mage’s spells, he’d also already made several wands of fireball) right on the command center that killed most of the leaders (though not the Baron), destroyed their #1 fear weapon and threw everyone into disarray.
Final score: withdrawal of remaining troops by one now-extremely homicidal but impotent maniac Baron, reluctant withdrawal of troops by one “ally”, one saved province, and one pissed-off GM.
He didn’t learn his lesson, however, and we were later able to successfully besiege a castle using almost exactly the same strategy.
Stockpile Raid. Lots of Raid.
Irritated GM’s can make bad things happen…lucky arrow shots, tragic failures of equipment, and miraculous saving throws can ruin a partys day.