Combine mushrooms, eggplant, zucchini, olive oil, salt and pepper in a large bowl; toss to coat. Transfer to rimmed baking sheet and roast for 30 minutes, stirring halfway through cooking time, or until vegetables are softened and just starting to brown. Set aside.
If you're planning on eating the manicotti the same day you make it, reduce oven temperature to 350 degrees. Otherwise, turn oven off.
Cook manicotti shells al dente, according to package instructions. Drain and run under cold water until shells are cool enough to handle.
While shells are boiling, in another large bowl, stir together ricotta, egg, salt and pepper. Fold in roasted vegetables, ¼ c. parmesan cheese, and ½ c. mozzarella cheese.
Spread 1 cup of marinara sauce on the bottom of a 9 x 13 casserole dish (use a freezer-to-oven safe dish if freezing). Using a small spoon, carefully fill each manicotti shell with cheese and vegetable mixture. Place finished manicotti in baking dish. Once all manicotti are filled, top with remaining sauce and cheese.
To make right away:
Cover casserole dish with foil. Bake manicotti at 350 degrees for 30 minutes, then remove foil and bake 10 minutes more.
Cover casserole dish with foil and refrigerate for up to one day. Bake at 350 degrees for 30-40 minutes or until heated through, then remove foil and bake 10 minutes more.
Place plastic wrap directly on top of manicotti to minimize freezer burn, then cover casserole dish with lid. Freeze for up to 1 month. To bake, preheat oven to 350 degrees; remove lid and plastic wrap and cover with foil. Heat for an hour, then remove foil and bake about 15 minutes more or until manicotti is heated through and cheese has melted.
If you don't have a freezer-to-oven baking dish, you can use a disposable aluminum baking tray instead.