Melt the butter in a large, deep sauce pan or casserole over medium heat.  Add the onions and cook, stirring occasionally, until very soft and beginning to brown, 30-45 minutes.
Add the stock, turn the heat to medium-high, and bring just about to a boil.  Turn down the heat so that the mixture sends up a few bubbles at a time.  Add the seasoning herbs, salt, pepper, and cook for 15 minutes.  Preheat the oven to 400 degrees F.  Fish out the parsley and thyme sprigs, if any.  Add a crouton to four ovenproof bowls.  Add a portion of soup and top with cheese.  Place the bowls in a roasting pan or on a sturdy baking sheet and bake for 10 minutes, until the cheese melts.  Serve immediately.