Bring a large pot of lightly salted water to boiling. Add farfalle and cook 10 minutes; drain and set aside.
Meanwhile, in a food processor, combine basil, 1/4 cup of the pine nuts and the garlic. With machine running, slowly add oil in a thin stream until well combined. Remove to a small bowl and stir in 1/3 cup of the Parmesan, the salt and pepper. Set aside.
In a large saucepan, melt butter on medium heat. Sprinkle in flour, whisking constantly for 2 minutes. Pour in milk, nutmeg and pesto, whisking until the liquid comes to a boil. Simmer until thickened, about 2 to 3 minutes. Remove from heat and stir in 11/2 cups of the mozzarella and remaining 1/3 cup Parmesan. Mix until smooth.
Stir in tomatoes and pasta. Fold remaining 1/2 cup mozzarella into mixture; pour into serving dish. Top with remaining 1/4 cup pine nuts.