I've always thought of it this way: a muffin is something you'd eat for breakfast while a cupcake is for dessert. The cupcake is likely a bit sweeter and with a lighter texture.
But this recipe (below) for Cocoa Muffins, from Leite's Culinaria (a wonderful recipe site), makes me wonder. They're described as "dense and chewy," and the recipe method (combine wets and dries separately, then mix) is certinaly muffin-like. But cocoa! Not for breakfast (at least, that I'd admit to).
What do you all think?