Preheat oven to 350 degrees Fahrenheit. Spread bread cubes on rimmed baking sheets and dry briefly in oven 5-10 minutes. Lightly toast pecan pieces in oven, until just fragrant (3-5 minutes). Place the bread in a large bowl.
In a large skillet, melt 1/4 cup (4 tablespoons) of the butter over medium heat. Add the bacon, cook until browned. Add the onions, and stir until they soften, about 8-10 minutes. Add the apples (or pears) and soften another 3-5 minutes. Add the herbs and pecans, salt and pepper, mixing thoroughly. Remove from heat. Add vegetable mixture to bread and toss well.
Whisk broth and eggs together and drizzle over mix. Toss well and let rest for about 5 minutes.
Generously butter the muffin tins, coating the sides and bottoms of the cups thickly. Spoon 1/2 cup of the stuffing mixture into each muffin cup, making certain to get a good mix of vegetables and bread in each cup. Using back of spoon or the bottom of a 1/4-cup, press well to compact the stuffing. Mound another 1/2 cup or so of the remaining mix on top of the stuffing in each cup, pressing well with your fingers to hold shape.
Bake until tops are golden and crisp, 20-28 minutes. Let cool and set in pan, approximately 15 minutes. Using a small sharp knife, loosen around the edges and remove from tin. Note: Any stuffing recipe can be turned into muffins, simply add beaten eggs (3-4 eggs per 12 cups of bread) just before baking, as detailed above.