Bota Alta
Tv. da Queimada 37, 1200-364 Lisboa
This restaurant has many tables and very close to each other. The portions are on the large side and the environment is one of a household. I would suggest you try Bacalau au bras.
O Corrido - Casa de Fado
Campo de Santa Clara 49, 1100-471 Lisboa
Here I had the best meal I ever had in Lisboa and the best part is that you can dine and watch/listen to fado. You can often find discounts for this restaurant by making a reservation through The Fork.
Pasteis de Belém
R. de Belém 84 92, 1300-085 Lisboa
The best pasteis de nata can be found in Belém. You will find a cue, but if you are willing to eat them on the go the cue is fast and worth doing.
Confeitaria Nacional
Praça da Figueira 18B, 1100-241 Lisboa
If you are on the hunt for pasteis de nata, but are not willing to go to Belém, this place is a great place where to have them and stop for a while. You can sit down and take your time.
Restaurante Senhor Peixe
R. Pimenta 35, 1990-254 Lisboa, Portogallo
If you are willing to adventure yourself outside the center of Lisboa, here you can have some great fish.