There used to be a antiquarian book fair held under the arcades at Praça do Comerçio on Sunday Mornings.but I think with the remodelling of the square this has now passed on.
There used to be several antiquarian booksellers in the area around Calçada de Carmo running up from Restauradores Station to Largo do Carmo. Some may still be there but with the economic crisis don't count on it.
There also is a wonderful bookshop in Cascais, (40 minutes by train from Lisboa Cais de Sodre Station) Livraria Galileu, which sells all sorts of 2nd hand books in Portuguese and other different languages!
Avenida Valbom 24-A
(3 minutes walk from Cascais Station)
I have had many a happy hour rustling through their piles in their basement storeroom.