Hi,
I'm dealing with the same dilemma (2 1/2 DS). Last time he flew was last November, so his interests have changed somewhat, but here is what I'm planning on for our Sept flight to WDW:
Clifford sticker books (I bought this two book pack at a discount warehouse store. I figure one book for the way down, one for the way back)
Crayons and a coloring book (my friend is taking color wonder markers, they mark on the special paper, but no where else, personally I cannot stand the smell, so I'm sticking with crayons)
One Fish, Two Fish, Red Fish, Blue Fish (it takes a while to read, and he will listen to it two times in a row)
Game Boy (we have a Blue's Clues game for him. He hasn't yet figured out how to play, but he's happy pushing the buttons).
SNACKS
Previously flights he has slept, walked the aisles with Daddy, flirted with the flight attendants. Actually, based on our last flight, my biggest concern is to stop him from kicking the seat in front of him!
Good Luck!