I made the huge mistake of not being prepared to bring WDW treats back home on the airplane my first trip. Two snack credits per day x 4 people x 10 days adds up to a LOT of snacks to bring home.
Many places do not package your snacks if you buy them over-the-counter. I got lucky when I stocked up on fudge at the MSB because they use boxes and those papers, but if you want to bring back a cupcake from the KB at AK or RS at MGM, good luck! I still haven't figured out a way to transport those huge cupcakes well.
Airlines will generally let you bring on food without it counting against your carry-on allowance. I just put all the snacks in reusable tote along with the meals for everyone for the trip and security doesn't differentiate between a box of fudge and a sandwich meal. I didn't want to risk the chocolate melting or spoiling if my bag was lost for any length of time.
Tupperware-like containers are a good idea, but the boma cake and resort dessert containers work well in a pinch too...albeit a very noisy solution.