As I posted yesterday, making individual pies in muffin or cupcake liners is a great way to make 'planned leftovers' from dinner look neat enough to put into a bento box. As Sile suggested in the comments, if you don't want to use throwaway paper cups, silicone cups are a reusable alternative. Calphalon makes a nice silicone liner and cupcake pan set which would be perfect for this. The liners are in pretty pastel colors.
You can also use the liners as dividers in your bento, for salads, fruit, and so on. They sell the tin and liners as a set, as shown here, or the liners on their own. Extras might be a good idea to have if you do freeze the food 'cupcakes'.