For Salsa: In an oven, broil the tomatoes, onion and garlic cloves, turning as necessary to blacken evenly. It should take only a few minutes. When these have blackened, peel the skin from the tomatoes and remove the papery skin from the garlic.
Add the vegetables to the work bowl of a food processor, along with salt, black pepper and the chipotle en adobo. One chipotle pepper makes a mild to medium salsa. Two make a fairly intense medium salsa. The remaining chipotles and sauce can be frozen in a well-labeled bag.
Pulse in the food processor until liquified. Pour the salsa into a shallow pan and cook on medium heat about five minutes, until most of the water has cooked out. Let cool and set aside.
For Quesadillas: Grease preheated waffle iron with nonstick cooking spray. Place the bottom tortilla on the waffle iron first, then spread desired amount of refried beans on tortilla and sprinkle with cheese and sauteed onions. Top with second tortilla. Close waffle iron and allow to cook until cheese has melted and tortillas are golden brown.
Serve roasted tomato salsa alongside quesadillas and dig in!