Pierce the bratwurst with a fork or the tip of a paring knife a few times on all sides and place them into a zipper sealable plastic bag. Combine the beer, molasses, honey and Worcestershire sauce, whisking gently to dissolve the molasses and honey. Pour the marinade over the sausages and seal the bag, shaking it gently to thoroughly coat the brats. Refrigerate for at least 6 hours or as long as overnight, turning the sausage over a few times during the marinating process.

Pre-heat a heavy skillet over medium-high heat. Remove the bratwurst from marinade and reserve ½ cup of the marinade. Sear the brats in the hot skillet on all sides until browned. Transfer the browned sausages to a plate and cover with foil.

Add the onions to skillet and sauté until lightly browned. If the skillet gets too dark on the bottom, simply stir in a few tablespoons of water. Season the onions with salt and freshly ground black pepper. Add the apples and thyme and continue to sauté for a few minutes. Add the reserved marinade to deglaze the pan. Return the bratwurst to the pan, nestling them into the onions and apples. Lower the heat and simmer for 10 to 15 minutes until the sausages are cooked through.

Serve the bratwurst, apples and onions with a side salad or over mashed potatoes with spicy mustard on the side.