Cut squash in half lengthwise; remove and discard seeds. Cut each half into 4 wedges; cut wedges into 2-inch pieces.
Stir together squash, 1/2 cup apple cider, and next 5 ingredients in a 12-inch, deep-sided, nonstick skillet over medium-high heat; bring to a boil. Cover, reduce heat, and simmer, gently stirring occasionally, 25 minutes. Uncover and cook 5 minutes or until liquid thickens and squash is tender. Gently stir in pecans and sage until well combined.
*3 lb. sweet potatoes may be substituted for butternut squash and 1/2 cup apple juice may be substituted for apple cider.