I was in Lisbon for a long weekend in 1999 and had a great time. For eating, we stuck to seafood, which is abundant and good.
Two restaurants stand out:
1. Take the commuter ferry from the Ferry Terminal across the Tagus River for 50 cents. This is worth doing anyway - you get a good view. On the other side, turn right and walk along the water 400 yards. It is all piers and warehouses but then there is this little restaurant with tables right on the water. They had good fish.
2. a really traditional place in Baixa whose name I can't remember.
We spent most our time in Baixa and Alfama. The latter is a more tradition area of narrow streets and little cafes.
The funicular (cog-railroad) that goes up the steep slopes is fun to ride on.
We also went to a restaurant that features Fado, the traditional portuguese singing. It is one of those typical tourist things to see.
For a list of trendier, higher-end restaurants see
here. I used Time Out's restaurant guide for Rome recently and was pleased. Lisbon's guide looks just as good.