After reading as many Lisbon-related posts from other Chowhounds, we visited a few great restaurants on our trip. As previously noted, Bonjardim is great (and the cuttlefish are as good as the chicken) as is Fidalgo. But we also found 2 nore places worth a visit.
It's called Velha Gruta (and right now its entrance is a little obscured by construction work, although they do have a big red banner out front to help you spot the place) and is on the very edge of the Bairro Alto neighborhood on the Parça de Luis Camões. We actually stopped in because every person in the place was eating with gusto and had a smile on his/her face-- always a good sign. We did too by the time we left; the food is a mix of Portugese and French and is slightly more expensive than most simple eateries (average main was about 9-10 Euros). The wine list is good, and they also do salads here, which is pretty unusual. Go for the chevre chaud salad or the beef. I also have to say that the service here was friendlier than anywhere else we visited in Portugal.
The Pois Café on Rua São João da Praça, 93-95 in the Alfama is also worth checking out-- it is unusual in that it seems much more like a Western European or North American coffee house than a typical Pourtugese bar-cum-restaurant-cum-café. It appears to be run by a cohort of 5 Austrian women. It's all very spacious and cool, and a cozy place to sit for a while to relax. Oh, and order the 'pois café', which comes with a surprise. Our surprise was a delicious slice of strudel.