Melt the butter in a very large (12-inch) saute pan and cook the onions over low heat for 20 minutes, or until tender but not browned. Add the zucchini and cook, covered, for 10 minutes, or until tender. Add the salt, pepper, and nutmeg and cook uncovered for 5 more minutes. Stir in the flour. Add the hot milk and cook over low heat for a few minutes, until it makes a sauce. Pour the mixture into an 8 by 10-inch baking dish.
Combine the bread crumbs and Gruyere and sprinkle on top of the zucchini mixture. Dot with 1 tablespoon of butter cut into small bits and bake for 20 minutes, or until bubbly and browned.