Melt butter in a Dutch oven over medium heat. Add onion to pan; cook 5 minutes, stirring frequently.
Reduce heat to medium low and continue cooking 50 minutes or until deep golden brown, stirring occasionally.
Add pepper, apple, thyme sprigs, and bay leaves; cook 3 minutes or until apples soften. Add wine; cook 2 minutes, scraping pan to loosen browned bits.
Add broth and cider; bring to a boil. Reduce heat, and simmer 45 minutes. Discard bay leaves; stir in vinegar.
Arrange bread cubes in a single layer on a jelly-roll pan; broil 2 minutes or until toasted, turning after 1 minute.
Preheat oven to 500°.
Ladle 1 cup soup into each of 10 ovenproof soup bowls. Divide the croutons evenly among bowls, and top each serving with about 3 tablespoons cheese. Place bowls on jelly-roll pan. Bake at 500° for 8 minutes or until cheese melts. Garnish with thyme leaves, if desired.