Saute onion and garlic in 3 quart saucepan until golden. Add mushrooms and cook until browned, about 5 minutes.
Add spinach to pan and heat through.
Puree tofu in a food processor. Add parmesan, salt, pepper, and nutmeg and blend. Pour mixture over spinach. Mix well and heat through.
OPTIONAL: boil manicotti in 4 quarts of salted water for one minute, and bathe in cold water. (This is the step per the original instructions, but I've never found it necessary to cook manicotti for a casserole -- and they are much easier to stuff when dry).
Stuff each manicotti with about 1/2 cup of the spinach mixture. Place in casserole dish and cover with marinara. Place foil over dish and bake 45 minutes.