Really good ideas on the running off energy ahead of time as much as possible. Where possible, flights around nap times are great, but often not realistic for many reasons. I swear by snacks, my little guy is happiest while eating, and especially anything that seems somewhat "Treat" like. We also bought a fruit frozen smoothie to share with my not quite 2 year old. He hadn't had one before, so it was a huge treat and helped avoid issues with his ears during takeoff. I also had a little bag of new things for them, variety was key as no idea what they would gravitate towards: stickers (esp the bigger foam ones), coloring pages and crayons, books to read to him, new little dinosaur and car figures, etc. Short attention spans were an important factor to consider.
And for in lines, I find food easiest. Both things we brought as well as the little grape packs you get with kids meals at WDW. Kept their tummies full, mouths occupied, and meant less time required for meal breaks (my kids are the slowest eaters ever).