In a large bowl combine the oats, wheat germ, almonds and cranberries and stir until thoroughly mixed and set aside.
In a small skillet, combine the butter, honey, molasses, brown sugar, cinnamon, ginger, cloves and salt and bring over medium heat. Stir and heat until ingredients are combined. Remove from heat and add vanilla. Stir to combine.
Pour the molasses mixture into the bowl with the oats and stir until the oats are completely coated. Place the bowl in the refrigerator and chill for 30 minutes.
Preheat the oven to 325. Lightly mist 12 cups in a muffin tin with cooking spray. Divide the granola mixture evenly among the muffin cups. Using your fingers, press the granola down into each cup and up the sides to from a cup. The mixture will be sticky so every few cups I rinsed my fingers in cold water to keep them from getting too sticky.
Bake the granola cups for 15-17 minutes. Remove from oven and allow the granola to cool completely before removing the cups from the muffin tin. The cups will firm while cooling. Once they are cooled, spoon in the filling of your choice. I filled mine with 3 tablespoons of fat free vanilla yogurt each and then topped them with berries.