Place the onions, thyme, pepper and butter in a 6 quart slow cooker. Turn the setting to low and let them go for 7-8 hours. The onions will become carmelized.
When the onions are soft and carmelized, remove the thyme sprigs. Add in the beef broth and wine. Turn the slow cooker to high for another 2 hours.
Just before the soup is done, taste for salt. Add as desired.
Make croutons for soup. Simply cut a whole grain baguette or your favorite bread into cubes and place under the broiler for a few minutes. Watch it because bread burns easily.
Make sure you put your soup into a ramekin or bowl that can go into the oven. Top each soup with some croutons and a 1/4 cup of cheese and place it back under the broiler. Let the cheese melt and get bubbly. Enjoy!