I n a large pot sauté the onions in olive oil until brown, then add peppers and allow to soften. Stir in whole garlic cloves, tomatoes and bay leaf and turn heat down to a simmer and leave for 10 minutes.
Meanwhile, in a separate pan, sautee eggplant and zucchini (they tend to get mushy if you throw them in with everything else but that can be good too and is easier than dirtying a second pan) until browned and softened.
Add the zucchini and eggplant to the simmering pot along with the sprigs of thyme and some salt and pepper (to taste) and allow to simmer at least another 20 minutes. Simmer longer if you want the flavors to really get good, or just reheat it the next day and you'll have the same effect.
Finish out the bay leaf and the whole garlic cloves and serve piping hot with crusty fresh baked bread or basmati rice. Add the minced garlic to the top of each serving.