Preheat oven to 350 degrees F (175 degrees C). Grease a 12 cup muffin pan or line with paper baking cups. Combine the soy milk and vinegar in a measuring cup. Let stand for about 5 minutes to thicken.
In a large bowl, stir together the peanut butter, oil, sugar, honey, vanilla and flaxseed meal. Mix in the soymilk. Combine the flour, baking powder, baking soda and salt; stir into the batter just until blended. It is okay for the batter to be slightly lumpy. Spoon the batter into the prepared cups, dividing evenly.
Bake in the preheated oven until the tops spring back when lightly pressed, 20 to 25 minutes. Cool in the pan set over a wire rack. When cool, arrange the cupcakes on a serving platter. Frost with desired frosting.