The Almond Biscuit Apartment above this historic Porto bakery is a real find. It's centrally located, well-equipped, comfortable and quirky, and includes a delicious breakfast each morning (except for Sunday) from the bakery below where you're staying. The light from the huge windows opening out onto the square is amazing, even on cloudy days, which are common in Porto.
I highly recommend this stay -- just be aware that you and your bags will be climbing up and down three flights of stairs every time you go in and out!