Bake the butternut squash: Preheat the oven to 350°F. Cut the butternut squash lengthwise in half and scoop out the guts and seeds and discard them (or save the seeds and toast them).
Pour 1/4 cup of water into a baking dish and place the butternut squash halves cut side down.
Bake for 40 minutes or until a fork easily pierces the squash. Allow to cool for 10 minutes.
Scoop out the squash flesh from the skins and put into a blender. Discard the skins.
Sauté the shallots in the olive oil over medium heat in a small skillet until just beginning to brown, about 2-3 minutes.
Purée in blender: Add the shallots to the blender. Add 1 cup water, the parmesan, 1 teaspoons salt and 1/8 teaspoon nutmeg and blend until smooth. Taste and add more salt if needed. If the sauce is too thick, thin it with a little more water.
Add sour cream and heat until warm: Pour the sauce into a small pot set over low heat. Mix in the sour cream and warm it through. Do not let the sauce boil.
Cook pasta in boiling salted water: Fill a pot with water and salt (1 tablespoon of salt for every 2 quarts of water). Set over high heat to bring to a hard boil. Add the pasta and cook at a hard boil, uncovered until al dente.
Mix cooked pasta with sauce: When the pasta is ready, drain and put it into a bowl. Mix with a little of the sauce and serve. Add a dollop of additional sauce and some parsley right when you bring it to the table