I started doing muffin tin lunches for my 3-year-old daughter (and now my 14-month-old son) for almost 1 1/2 years now. I love the fact that it challenges me to think outside the box with variety, but I've found a flaw. In order to save leftovers, I have to move them to a different container. The 6-cup muffin tins from Dollar Tree don't even fit into gallon-sized Ziplocs, so saving them in the tin isn't an option. Bummer.
Awhile back I was browsing Inchbug ordering some cup labels for the kids, and I saw these containers. There are a ton of different food storage options on that site, but these fit the bill for us perfectly. They have a snap-on lid for the dip portion and the whole thing making it perfect for lunches on-the-go and for storing leftovers. We use the middle portion for yogurt, peanut butter, hummus, ranch dressing, etc. Then I just fill the outside with a handful of other things - celery sticks, baby carrots, PB and honey sandwiches (cut into stars above), apple slices, cheese sticks, and the list goes on and on. My 3-year-old loves the containers (something about giving lunch to her in a compartmentalized tray appeals to her), and I love the convenience of not having to dirty yet another container for leftovers. These are also much easier to clean than the muffin tins which do not hold up well in the dishwasher.
Hope you find these as helpful as I have!