If you're not using all the cups in a muffin tin, put an ice cube in each unused cup to even out the heating and protect your pan from burning.
p.s. Those silicone baking dishes are bunk. They don't get hot enough to give anything a good enough browning, and they're a pain to stand up in the dishwasher.
EDIT: (10/4/08) Linda B gave an excellent suggestion for silicone muffin pans in the comments of this post: "The silicone muffin cups are great for poaching eggs en masse, though. That's what I use them for. Just a little spoon of water in each one, then break an egg into each one, season, and cover with foil. Bake at 350 for 10-20 minutes (depending on how firm you want them) and voila! A dozen poached eggs!"