My daughter and I just went on a 3 hr flight a month ago (she is almost 3 also very very active too).
We did not have a DVD player but that would have been nice, even if it only last for 30 mins.
The seats that I found to be the BEST are the window and middle seat, this way you can sit in the middle & son by window and looking out the window can keep their interest for awhile. Also easier to keep everything contained.
IDEAS:
* Etch-A-Sketch (mini/travel size)
* Old deck of cards (can play with & color on), you want it to be a deck you don't mind losing a few cards, I am sure we lost a few on our last trip
* Crayons in a zip lock bag
* paper/coloring book
* cheap stickers/band-aids that he can stick to himself, coloring book or small note pad
* little NEW books
* some cheap but new toys (I went to the dollar store, got some little dinosaurs and other little toys that I actually tossed when we got home, or packed away for a future trip)
* If you are by the window (and he/you are ok with looking out the window) you can point out different things you see (clouds, farms, green land, brown land, rivers and such)
* We also looked through the magazines that are in the front pocket and played a game (can you find a shoe, a man with blond/yellow hair and so on)
*I also had bought tons of little snacks to help break the time up (ever 30 mins some different little snack like a sucker, cookie, gummy bears, goldfish crackers and so on)
You did not mention how long the flight is but at those are the ideas I have and used on our flight. Lastly even if things get crazy try to stay positive, I found that when I started to get frustrated/tired my daughter would start to get cranky making everything worse but as soon as a took a deep breath (also told my daughter to take one with me) we both felt better. Go with the follow and allow enough time to get through everything.