Melt butter in large pot over medium heat. Add onion and saute until just tender, about 8 minutes. Add squash, cover, and cook until beginning to soften, about 6 minutes. Add apples and vegetable broth (or water), cover, and simmer until vegetables are soft, about 12 minutes.
Add cinnamon. Cool slightly. Working in batches, transfer to a food processor and puree until smooth. Add more liquid if too thick. Season to taste with salt and pepper. Transfer to serving bowl. Sprinkle with raisins.
Serve warm, or cover and refrigerate without raisins (can be made up to 2 days ahead). Reheat over medium heat and sprinkle with raisins.