Crayola makes these really cool markers called Color Wonder. They will only work on Color Wonder paper. A tad expensive, but we only use them while travleing. They will NOT write on tray tables, windows, seats, nothing but their own paper. Very cool stuff.
I will also admit to a small dose of Benadryl for DS, but in his case, all 3 times we have flown with him, he has had an ear infection. So right before boarding, he gets benadryl, and ibuprofin along with his antibiotics.
I have also heard of folks having great luck keeping toddlers occupied with masking tape (make balls of it, put it all over, whatever) and pipe cleaners(oh, excuse me, Chenille Stems as they are called in our PC society these days.

they are light, easy to pack, make almost anything with them.