Preheat the oven to 400°F. Place the feta in an ovenproof baking dish and cover with aluminum foil. Bake for 15 minutes.
Stir together the tomatoes, shallots, garlic, olives, capers, lemon juice, olive oil, parsley, thyme, oregano, and red pepper flakes in a medium bowl to combine. Season with salt and pepper, to taste. Remove the foil from the feta and spoon the tomato mixture over the top. Bake for another 15 minutes, until the feta is tender and the tomatoes are softened. Serve warm with crackers alongside.