Preheat oven to 325 degrees F (165 degrees C). Line a 9x13 inch baking dish with aluminum foil, extending the foil sheets over the side of the dish.
To make the crust, mix the graham cracker crumbs, butter, and 2 tablespoons brown sugar together in a bowl until evenly blended. Press evenly over the bottom of the prepared baking dish.
To make the filling, beat the cream cheese, 1 cup brown sugar, and vanilla together in a mixing bowl until evenly blended. Beat in the sour cream. On low speed, add the eggs, one at a time, just until blended. Pour the mixture over the crust.
To make the topping, place the apples in a bowl, and toss with 1/2 cup brown sugar, pecans, and cinnamon until evenly blended.
Bake in preheated oven until center is almost set, about 55 minutes. Cool, and refrigerate 4 hours, or overnight.
Before cutting, allow the cheesecake to sit 30 minutes at room temperature, then lift from the baking dish using the extended aluminum foil sheets, and place on a cutting board or serving plate. Remove the aluminum foil, and cut into 16 squares.
