Prepare pasta according to package directions BUT reduce cooking time by a couple of minutes so the pasta will not overcook during baking time. Drain, separate, and lay out on a sheet pan so it doesn't stick together and set aside (wax paper or parchment paper can be used to layer pasta on the pan).
While the pasta is cooking, saute the spinach, green onion, and garlic in oil over medium heat in a large skillet until spinach is wilted. Drain spinach if needed and transfer to a plate lined with paper towels to cool.
In a medium bowl, mix the ricotta, egg, parsley, and nutmeg. Coarsely chop the cooled spinach and mix into the ricotta mixture. Stir in parmesan and mozzarella.
Put cheese mixture in a resealable bag (quart size may be easier to handle). Cut enough of the bottom corner of the bag to create a quarter-sized whole. Place corner of bag into the opening of manicotti noodles and squeeze mixture into half the noodle, turn noodle over and squeeze into the other end to fill. (It may take a little practice, but you'll get the hang of it!)
Discard wax/parchment paper. Spread a little marinara in the bottom of a 13 × 9-inch baking dish and layer the stuffed manicotti on top of the sauce. Ladle marinara or spaghetti sauce evenly over pasta. Sprinkle with additional Parmesan cheese, cover with foil, and bake for 30 minutes.
NOTE: The stuffed noodles can be frozen until ready to bake. Once frozen, manicotti can be transferred to a vacuum seal or reclosable bag for long-term storage.
Use a meat sauce in place of the marinara
Pipe cheese filling onto cooked lasagna noodles and roll up as a substitute for tubed pasta
Top with mozzarella instead of Parmesan before baking
Substitute wheat-based pasta for the gluten-free pasta (both have been tested for this recipe)
Substitute Grana Padano cheese for the Parmesan (use mozzarella for the topping)
Mix in mascarpone or goat cheese for part of the ricotta
Substitute Fontina or Swiss cheese for the mozzarella. I don't recommend fresh mozzarella due to its higher water content.
Substitute frozen spinach for fresh spinach. A rough estimate for substitution: 8 ounces fresh = 3/4 cup cooked = 5 ounces frozen. Frozen spinach contains a little extra water so defrost it first and squeeze out any excess water.
Substitute arugula, beet greens, Tuscan kale, or Swiss chard for the fresh spinach
Substitute minced shallot or leeks for the green onion.