Preheat the oven to 325 degrees F.
Cook cranberries, ½ cup of the sugar, 4 tablespoons of the orange juice, nutmeg, and cinnamon in a saucepan set over medium heat until the cranberries begin to pop and mixture thickens, stirring occasionally. Cool slightly.
Process the cranberry mixture in a food processor until smooth; transfer to a bowl. Stir in 1 tablespoon of the vanilla extract. Refrigerate until ready to use.
Mix the cookie crumbs and butter; press 1 tablespoon onto the bottom of each of 24 paper-lined muffin cups.
Beat the cream cheese and remaining sugar in a large bowl with a mixer until blended. Add the sour cream, orange zest, remaining 1 tablespoon orange juice, and the remaining 1 teaspoon vanilla extract; mix well. Add the eggs, 1 at a time, mixing on low speed after each just until blended. Add ⅔ cup of the cranberry mixture; swirl gently. Spoon ⅓ cup of the batter over the crust in each muffin cup.
Bake 25 minutes or until the centers are almost set. Cool. Refrigerate for at least 2 hours.
Drizzle with the remaining cranberry mixture and top with some whipped topping just before serving.