I disagree with some of the other answers. There are still a lot of incredible, nice libraries and bookshops, with passionate and expert people. Fnac and Gibert are not so great to visit, but why not.
Gibert can be a bit interesting tho, as it is big and has a lot of books and themes (they did not "reduced in size quite drastically" as @jcaron said). And their employees can be pretty good.
The nice, historical shops did not close, the great majority still are there, standing. Their employees have a great knowledge of recent, old and specialized literature and books most of the time, which is not the case in supermarkets like the fnac.
For philosophy, J.Vrin, founded in 1911 near the Sorbonne is very nice, with a good atmosphere, all classics and recent philosophy publication. They have 3 shops near the Sorbonne. Their vendors all are experts from what I have seen.
The Librairie Delamain, said to be the oldest of Paris (founded in 1700, moved in 1900) is an historical monument and is still opened. It was frequented by very famous authors and presidents of France (Coctau, Aragon, Miterrand). Beautiful.
Galignani, founded in 1911 has a nice 1930 decor and atmosphere. Knowledgeable sellers and classical foreign and french books. Lot of art books.
There are dozains of wonderful places like those. Here you can find more.
I personally recommend l'ecume des pages (near Saint-Germain) and l'arbre du voyageur (near Mouffetard). La compagnie du livre near the Sorbonne is also really interesting.
The price of the unused / new books is the same everywhere in France so no reason to go to ugly supermarkets with less books than classical, wonderful libraries for the same price imo.
For comics and european 'bande dessinée' the Album shops are really cool, a lot of choice and the vendors are nice and know their job :)