Preheat oven to 325 degrees F. Line a 12-cavity (regular-sized) cupcake pan with paper liners and set aside. Blend whole Oreos in a food processor or powerful blender to form crumbs. (Make sure the crumbs are all even-sized and you don't have big pieces.) Do not remove the vanilla creme in the Oreos before blending.
Combine the cookie crumbs and melted butter. Divide the mixture between the cupcake liners (about 1 tablespoon per cup) and press into the bottoms. I like to use the lid of a milk container to press the crust into the bottoms evenly.
Bake crusts for 5 minutes then remove from oven. Set aside to cool.
CHEESECAKE FILLING AND TOPPING
Make sure the cream cheese, sour cream, and eggs are all at room temperature. Reduce the heat to 300 degrees F.
In a large bowl, combine the cream cheese and white sugar with a hand mixer. Beat at low speed and in the same direction (to avoid cracks later on). Add in the sour cream, vanilla extract, and sea salt. Beat on low speed until completely combined.
Scrape down the sides and add in the flour. Beat on low speed until combined. Add the first egg and beat until the egg is completely incorporated. Add the second egg and again, still beating slowly, beat until combined.
Blend another 5 whole cookies in a food processor or powerful blender to form crumbs. Do not remove the vanilla creme in the Oreos before blending. Gently fold the crumbs into the cheesecake mixture with a spatula.
Divide the batter evenly between the cupcake liners and fill most of the way. You should use all of the batter between the 12 cupcake liners.
Bake cheesecakes for 13-16 minutes, or until there is just an ever-so-slight jiggle in the center. Then turn off the oven and leave the door closed for another 10 minutes. Crack the oven door and allow cheesecakes to cool for 25 minutes longer, and then remove and place on the counter at room temperature.
Once the cheesecakes are at room temperature, transfer to the fridge to chill for 2-3 hours.
Refrigerate until ready to serve.
Chocolate Ganache
Place the chopped chocolate in a heat-safe bowl. Bring the heavy cream to a simmer on the stovetop, stirring occasionally. Just as soon as you see a simmer, remove from the heat and pour over chocolate chips. Place a plate or lid over the chocolate and cream mixture and let sit (without touching) for 5 minutes. Remove the plate or lid and whisk the chocolate until it becomes smooth.
Let the ganache sit for about 15 minutes to thicken and set. Spoon over the top of the cheesecakes. (Don't add ganache to any cheesecakes that won't be eaten the same day). Store ganache and cheesecakes separately.