Preheat your oven to 350°F (175°C).
In a large bowl, whisk together the flour, baking soda, cinnamon, ginger, nutmeg, and salt.
In another bowl, cream the softened butter and brown sugar until light and fluffy.
Add the eggs and molasses to the butter mixture, mixing until combined.
Gradually add the dry ingredients to the wet mixture, stirring until just combined.
Spoon the batter onto a lined baking sheet, making small mounds.
Bake in the preheated oven for 10-12 minutes, until set.
Allow the whoopie pies to cool completely on a wire rack.
While cooling, prepare the cream filling by beating together the cream cheese, powdered sugar, and ground ginger until smooth.
Once the pies are cooled, spread or pipe a generous amount of filling onto the flat side of one cookie and top with another.
Store the assembled whoopie pies in an airtight container for up to five days.