Preheat the oven to 325°F.
Place cupcake liners in a cupcake pan and spray with non-stick cooking spray.
In a small bowl, combine graham cracker crumbs, sugar, and melted butter. Place about 1 ½ tablespoon of the mixture into each cupcake liner and press into the bottom. Bake for 5 minutes, then remove from oven and allow to cool.
Reduce oven temperature to 300°F.
To make filling: In a mixing bowl, beat cream cheese, sugar and flour on low until just combined. Scrape down the sides of the bowl, then add sour cream and vanilla. Beat on low again until combined. Beat in eggs one at a time, scraping down the sides of the bowl after each is mixed in.
Divide batter equally into 6 bowls, about ½ cup per bowl. Add one color of gel food coloring to each bowl, Red, Yellow, Orange, Blue, Green, and Purple. Stir each to blend.
Start layering the colored batter by adding about 2 teaspoons of red batter into each cup. Once the red batter is evenly distributed, add the orange batter in the center of the red. Repeat this process with the remaining colors, yellow, green, blue, and purple. The cups should be almost full.
Bake for 18-20 minutes, then turn off the oven and leave in for another 10 minutes. Crack the door open and allow the cheesecakes to cool in the oven for 15-20 minutes. Place in the refrigerator to finish cooling. Let chill for about an hour.
To make whipped topping: Beat whipping cream, powdered sugar and vanilla in a medium sized bowl until stiff peaks form.
Using a piping bag with your choice of tip, pipe whipped cream onto cheesecakes and serve immediately.