Line a standard cupcake pan with paper liners and preheat the oven to 325°F.
Mix graham cracker crumbs, cinnamon, and sugar. Stir in melted butter and press 2 tablespoons into each liner. Refrigerate crusts.
Prepare streusel by combining flour, brown sugar, oats, cinnamon, and nutmeg. Add melted butter and stir until coarse crumbs form. Chill in refrigerator.
Beat softened cream cheese with sugar, vanilla, and flour until smooth. Add the egg and mix just to combine.
Spoon cheesecake filling over crusts, filling about two-thirds full.
Toss chopped apples with lemon juice, brown sugar, cornstarch, cinnamon, and nutmeg.
Spoon apple mixture over the cheesecake filling and gently press it down.
Generously sprinkle the chilled streusel topping over each cheesecake.
Bake for 28 to 30 minutes until the edges are set.
Cool cheesecakes in the pan for 30 minutes, then refrigerate until chilled.
Serve topped with caramel sauce.