In order of preference, mine only: Tomar (Templar Castle), Fatima (a detour, but worth it for some folks), Coimbra (major university with an outstanding library of ancient manuscripts as well as stunning architecture). If you can't see them all, look at some of the guidebooks referenced above and decide what interests you most. Train service is pretty good all the way to Tomar, so you can pick and choose where to get on/off and walk between Lisboa and Tomar.
My only regret is that I decided not to visit Nazare, which is (has become?) one of the greatest natural surfing spots in the universe, due to the underwater offshore canyon leading to a wave break that can be 70-100 feet tall when conditions are right. As someone who lives 1/2 time on Hawaii, my oversight was inexcusable and I'll be rectifying it when I return to walk the Portuguese Caminho again in a couple of years.
Bom Caminho.