Mix apple cider vinegar and milk in a medium-sized bowl. Let sit for five minutes. (This causes it to act like buttermilk.)
Whisk together flour, sugar, baking powder, baking soda, and salt in a large bowl.
Add the truffle oil, vegetable oil, and honey to the apple cider vinegar/milk mixture.
Pour the wet ingredients into the dry ingredients and stir well.
For the ganache, mix the truffle honey and heavy whipping cream in a small bowl.
Melt the chocolate on the stove or in the microwave.
Pour the melted chocolate over the truffle honey/heavy whipping cream and mix well.
Mix 1/4 cup of the ganche into the cupcake batter.
Fill cupcake liners 3/4 full.
Bake for 20 minutes or until the cupcakes bounce back when touched lightly.
When the cupcakes are cool, frost with the remaining ganache. The easiest technique for this is to dunk the top of the cupcake into the bowl of ganache and to twist your wrist slightly as you pull the cupcake out of the bowl. If necessary, microwave the ganache for about 20 seconds to make it easier to work with.
Optionally, drizzle some melted white chocolate on top of the dark chocolate and top with a chocolate truffle.