Preheat oven to 400°.
Pierce squash with a fork. Place squash on a baking sheet; bake at 400° for 1 hour or until tender. Cool. Cut squash in half lengthwise; discard seeds. Scrape inside of squash with a fork to remove spaghetti-like strands to measure 4 cups.
Heat olive oil in a large saucepan over medium heat. Add garlic; cook 2 minutes, stirring frequently. Add 1/2 teaspoon salt, 1/4 teaspoon black pepper, crushed red pepper, tomatoes, oregano, and thyme sprigs; bring to a boil. Reduce heat, and simmer for 20 minutes or until thickened, stirring occasionally. Discard oregano and thyme sprigs.
Combine remaining 1/2 teaspoon salt, remaining 1/4 teaspoon black pepper, Parmesan, and remaining ingredients. Spoon 1/2 cup squash into each of 8 (8-ounce) ramekins. Spoon tomato sauce evenly over squash; divide ricotta mixture evenly among ramekins, spreading to cover. Bake at 400° for 50 minutes or until lightly browned.