Preheat oven to 425°F Combine butternut squash, onion, olive oil, nutmeg, salt and pepper in large bowl. Spread on a rimmed baking sheet. Roast until squash and onion brown slightly, stirring occasionally, about 25 minutes. Allow to cool. At this point, butternut squash and onion mixture can be frozen. Defrost in refrigerator for several hours or in the microwave.
Combine defrosted squash and onion mixture, water or stock, butter and cranberries in a large saucepan and bring to a simmer. Add couscous and cover. Take from heat and let stand for 10 minutes. Stir in pecans and parsley and season to taste with salt and pepper. Fluff with a fork and serve.