Preheat the oven to 400°F (200°C).
For individual portions, divide the tomatoes, red bell pepper, red onion, garlic, and feta evenly among four oven-safe ramekins. Drizzle each serving with 1 tablespoon of olive oil.
For one large baking dish, add the tomatoes, red bell pepper, red onion, and garlic to the dish. Place the feta in the center and drizzle the olive oil over the feta and vegetables.
Combine the oregano, sea salt, thyme, black pepper, and red pepper flakes in a small bowl.
Sprinkle the seasoning mixture evenly over the feta and vegetables.
If using ramekins, place them on a baking sheet. Bake for 25 minutes, until the tomatoes have softened and the feta is warm and creamy.
Remove from the oven and stir the roasted feta and vegetables together. Add the chopped spinach and stir until evenly distributed.
Make one well in each ramekin. If using a large baking dish, make four separate wells. Crack one egg into each well.
Return the Baked Feta Eggs to the oven and bake for about 10 minutes, or until the egg whites are set and the yolks have reached your preferred doneness.
Sprinkle with fresh basil or chives, if desired.
Serve warm with crusty baguette, toast, or pita for dipping.