We've flown quite a bit with DD3, since she was 6 months on up.
The worse part for us is going through airport security. Our watches and phones are in a ziplock bag until we get through security so we don't have to scramble to take things off. My husband usually has the job of putting everthing in the bins, and I try to consolodate everything so we don't have a zillion small bags to put on the conveyor belt. I take DD and I'm in charge of folding the stroller. Sometimes we're in the line with the "small" machine and either the stroller or car seat won't fit in.
We normally try to book flights during nap time, so she'll sleep during the flight.
For take off and landing, we give her something to drink. Went from using bottle, to sippy cup, to juice box. One word of caution about juice boxes-- if there's still liquid in the box, sometimes the change in air pressure will make the juice squirt out the straw- I ended up with a very wet, sticky leg b/c I didn't realize this!
Lollypops helped at take off too. I just buy the small dum-dum sized ones, or the Safe-T-Pops. Those are the pops that have a looped stick, not a hard one so kids can't poke themselves. They make Winnie-the-Pooh ones now, which my daughter loves. Pops are saved as special treats for my daughter, so she'll readily take one if offered.
We bring a DVD player, but only take it out for emergencies-- don't forget headphones! Planes are usually noisy enough that it'll be difficult to hear the audio, or you'll have to turn it up very loud and it'll disturb other passengers.
Try on the headphones before getting on the plane, since not all styles will fit little heads! We ended up getting cheap "old-school" headphones from Radio Shack. A lot of the newer styles won't adjust small enough. Many portable DVD players have two earphone jacks.
I take off her shoes so she won't kick the poor passenger seated in front of her.
I also started making up activity bags for the past few trips. I try to find a zippered bag to keep things easily contained and just fill it with things to keep her busy. Foam stickers, small coloring book, construction paper pad, multi-color pens, decorated scotch tape, and crayons. Anything new-to-her is good! We take the activity bag into the parks with us too, so she is occupied while waiting in line (I only take one or two things though).
I've seen nice boxes of Disney crayons at the dollar store and
WalMart. There was a Winnie the Pooh and Princess version. The crayons snap into the case, so you don't have to worry about them rolling out all over the place as soon as the box is opened.
Another thing we do since we take the car seat on the plane-- when (if) they allow people traveling with children to board, my husband will go first and set up the seat for DD. I wait with DD until the final rows are called at the gate and then board so we don't have her restlessly sitting on the plane the whole time. She'd much rather run around for a bit at the gate.
I usually bring a small blanket, since not all planes have them available. It can get chilly and if DD will nap, a blankie is required!
We try hard to be engaging during the whole flight. Husband and I will make up stories and get silly with DD to make time pass more quickly.
All of our flights have gone really well (even my solo w/DD ones!). People around us usually say they didn't realize she was sitting right there b/c she was so quiet and well behaved.
Oh, and TONS OF SNACKS! We bring granola bars, forbidden sugary dry cereal, gold fish, animal crackers, and fruit gummies. We try not to give her too much to drink so we can avoid the bathroom on the plane.
Good Luck!
Crayola ColorWonder markers. They come in kits, or you can buy the markers and the paper/coloring books seperately. When DD was 2.5, we flew across country alone together on FF miles (= 2 layovers each way), and these things were a lifesaver! She loved coloring and I didn't have to worry about reimbursing Delta for new upholstery 
