Place two racks in the upper and lower thirds of the oven and preheat to 375 degrees F. Spray a mini-muffin tin generously with cooking spray.
For the chive creme fraiche: In a small bowl, combine the creme fraiche, chives, lemon zest and juice, salt and pepper. Refrigerate while you make the frittatas.
For the frittatas: In a large bowl, whisk the eggs, milk, creme fraiche, chives, dill, salt and pepper to blend well. Stir in the smoked salmon. Fill the cups of the prepared muffin tin 3/4 full with the egg mixture. Bake until the frittatas are puffed up and just set in the center, 8 to 10 minutes. Use a rubber spatula to loosen the frittatas and slide them onto a platter. Serve immediately with a dollop of chive creme fraiche.