Put bacon into a non-stick frying pan. Place over medium heat, cook 3 minutes or until light golden, remove from the heat. Stir in onions and set aside to cool for 10 minutes.
Preheat oven 200°C fan forced. Use a 9cm round cutter to cut 16 rounds from the pastry. Use the pastry rounds to line the base and sides of eight, lightly greased, 80ml (1/3 cup capacity) muffin holes.
Beat eggs and sour cream together with a fork until well combined. Add the bacon, cheese and thyme then spoon the mixture into the pastry. Top with tomatoes. Season.
Bake for 25-30 minutes or until pastry is puffed and golden and filling set. Stand 10 minutes in pan before transferring to a wire rack. Repeat with remaining pastry and filling to make another 8. Serve warm or room temperature scattered with herbs.