Preheat the oven to 350 degrees F. Line a muffin pan with paper liners.
Place the rum and raisins in a small pan, cover, and heat until the rum boils. Turn off the heat and set aside. Place the butter and molasses in another small pan and bring to a boil over medium heat. Pour the mixture into the bowl of an electric mixer fitted with the paddle attachment. Cool for 5 minutes, then mix in the sour cream and orange zest.
Meanwhile, sift the flour, baking soda, ginger, cinnamon, cloves, and salt together into a small bowl. Mix with your hand until combined. With the mixer on low speed, slowly add the flour mixture to the molasses mixture and mix only until smooth. Drain the raisins and add them and the crystallized ginger to the mixture with a spatula.
Divide the batter among the muffin pan (1 rounded standard ice cream scoop per cup is the right amount). Bake on the middle rack of the oven for 25 to 30 minutes, or until a toothpick comes out clean. Cool for 10 minutes before removing from the pan.
For the frosting, mix the cream cheese, butter, orange zest and vanilla in the bowl of an electric mixer fitted with the paddle attachment until just combined. Add the sugar and mix until smooth.
When the cupcakes are cool, frost them generously and garnish with a slice of crystallized ginger.
2009, Ina Garten, All Rights Reserved