Boil the gnocchi (if needed): If using homemade gnocchi, you can skip this step. If using hard store-bought shelf-stable or frozen gnocchi, drop them into a pot of boiling salted water and cook just until they float to the surface (about 2 to 3 minutes), then drain well.
In a medium saucepan over medium heat, melt the butter. Whisk in the flour and whisk until the flour turns golden brown, about 3 minutes. Add the warm stock and milk, and continue to whisk until it thickens, about 3 minutes. Stir in the salt, nutmeg, and sage.
Add the Fontina and Parmesan cheese a handful at a time, stirring in between additions until completely melted and the sauce is smooth.
Stir in the gnocchi, transfer the mixture to a baking dish, and bake for 20 minutes until the top is bubbly and golden.
Serve warm, topped with a little extra grated Parmesan cheese.