Older kids:
Ds's and games
crafty things - coloring books and markers, Bendaroos, etc
Younger - stickers and paper. Laptop for movies (or blackberry or phone or ipod - whatever you might have). For little ones, sometimes those big screens on the roof are impossible to see, and often the live personal sattelite TV's didn't have anything on that she wanted to watch...
Our coloring books are Color Wonder by Crayola - color on the paper, but not on clothes, seats, skin, parents, etc...
We've flown quite a bit in the last few years. Typically, each child gets a new DS game, plus various other "dollar store" type "presents", which are hidden and wrapped up in their backpacks (I use plastic grocery bags to wrap them in - also a good place to put the trash since airplanes still don't have a decent place to dump all the garbage a small child generates in 4 or 5 hours...) Only when they are given permission are they allowed to choose a "present" to unwrap. We usually try to space it out so they open one present per hour.
They also pack tons of snacks.
Some "present" ideas - travel games (battleship, trouble, cards, etc...)
hot wheels cars (can be lost easily, but who cares - $2 for 20 minutes of playtime is worth it for me!

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McDonald's toys (when it's something the kids like (hot wheels, barbie, etc...) I go up to the counter and buy one of each toy, then hide them till our next trip)
Sticker books - especially Disney themed ones - a great way to "get into the spirit" before you arrive.