Preheat the oven to 350 F.
In a small bowl, toss together the cherries, almonds, wheat germ, brown sugar, cinnamon and nutmeg until all the ingredients are evenly distributed. Set aside.
The apples can be left unpeeled, if you like. To peel the apples in a decorative fashion, with a vegetable peeler or a sharp knife, remove the peel from each apple in a circular motion, skipping every other row so that rows of peel alternate with rows of apple flesh. Working from the stem end, core each apple, stopping 3/4 inch from the bottom.
Divide the cherry mixture evenly among the apples, pressing the mixture gently into each cavity. Arrange the apples upright in a heavy ovenproof frying pan or small baking dish just large enough to hold them. Pour the apple juice and water into the pan. Drizzle the honey and oil evenly over the apples, and cover the pan snugly with aluminum foil. Bake until the apples are tender when pierced with a knife, 50 to 60 minutes.
Transfer the apples to individual plates and drizzle with the pan juices. Serve warm or at room temperature.