Preheat the oven to 400°F (200°C).
For individual servings: Divide the tomatoes, bell pepper, red onion, garlic, and feta evenly between four oven-safe ramekins. Drizzle 1 tablespoon olive oil over each.
For one large dish: Add the tomatoes, bell pepper, red onion, and garlic to the baking dish. Place feta in the center and drizzle olive oil over everything.
In a small bowl, mix oregano, salt, thyme, black pepper, and red pepper flakes. Sprinkle evenly over the feta and vegetables.
Place ramekins on a baking sheet or put the baking dish directly in the oven. Bake for 25 minutes.
Remove from the oven and stir gently so the feta mixes with the vegetables. Add the spinach and stir until slightly wilted.
Create wells in the mixture and crack one egg into each well.
Return to the oven and bake for another 10 minutes, or until egg whites are set and yolks are cooked to your preference.
Top with fresh herbs if desired and serve warm with bread for dipping.