The onions in this dish aren't just for show; the long roasting time brings out their sweetness and makes them delicious in their own right, and they add just the right savory note to the stuffing inside.
Preheat oven to 400 degrees. Slice off tops and bottoms of onions, leaving at least a 2-inch diameter exposed at the top. Scoop out the inside of each onion (about halfway down) using a melon baller or a spoon. Season insides with salt. Transfer onions to a baking dish, and cover with parchment, then foil. Bake until just starting to soften, about 1 hour.
Meanwhile, melt butter in a large skillet over medium heat. Crumble sausage into skillet, and cook, stirring, until almost cooked through, about 3 minutes. Add apple and fennel seeds, and cook until sausage is no longer pink, about 2 minutes.
Drain sausage mixture, reserving juices in a medium bowl. Finely chop sausage mixture, and add to bowl. Stir in breadcrumbs, parsley, sage, and 1/4 cup Gruyere. Let cool.
Fill onions with stuffing (about 3 tablespoons each), then top with remaining 1/2 cup Gruyere. Bake until tops are crisp and brown, about 20 minutes more.
Stuffing can be refrigerated for up to 1 day.