For the pies: Preheat the oven to 350 degrees F.
In a medium bowl, combine the flour, baking powder, baking soda, cinnamon, nutmeg and salt. In a large bowl with an electric mixer on medium speed, cream the granulated and brown sugars and butter until light and fluffy, scraping the side of bowl when needed. Add the eggs, and vanilla, beating well. On low speed, add the flour mixture and mix just until incorporated. Add the oats and mix 2 or 3 three times. Do not overmix.
On 2 baking sheets lined with a parchment or nonstick baking mats drop the dough in 1 tablespoon scoops 2 inches apart. (About 9 scoops per baking sheet.) With the bottom of a glass, gently push down on each portion to form a 2-inch disc. Bake until the edges are light brown, 8 to 12 minutes. Remove the pies to cool on wire racks and repeat with the remaining dough.
For the marshmallow filling: In a medium bowl with an electric mixer on medium speed, beat the marshmallow creme, confectioners' sugar, butter and vanilla extract until light and fluffy.
To assemble the pies, spread a heaping tablespoon of marshmallow filling on one cookie and sandwich with another cookie. Repeat until all the pies are filled.
Bring a small saucepan with 1 cup water to a simmer. Place a heatproof bowl over (but not in) the water to create a double-boiler. Add the chocolate chips to the bowl and stir until melted. Drizzle the melted chocolate back and forth over each assembled whoopie pie. Let set before serving.