Preheat oven to 400F. Cut the squash in half and remove seeds and strings. Sprinkle with salt and pepper and place face-down on an oiled baking sheet (I used a silicone sheet liner). Bake for 30 minutes, or until tender. (Different types of squash will take different lengths of time. Test by piercing with a fork in thickest areas.) Remove from oven but keep oven turned on.
While the squash are cooking, prepare the lemon-herbed rice. Heat a non-stick pan and sauté the onion until it begins to brown, about 5 minutes. Add the garlic and cook for another minute. Add the rice, 1/4 cup water, lemon juice and zest, soy sauce, and herbs. Stir well, cover, and cook on low heat just until warm. Add the toasted pine nuts and salt and freshly ground black pepper to taste.
Stuff the rice into the cavities of the squash. Place them upright in a baking dish and drizzle about a teaspoon of water over each. Cover tightly with aluminum foil and bake for about 20 minutes, until hot throughout. Serve warm, garnished with additional fresh herbs, if desired.