Amsterdam has two book shop institutions: Atheneum and De Slegte. Atheneum is your intellectual paradise, with a big section of foreign language books as well all the Dutch novels. I was last in there trying to buy a French novel for my French night school teacher and found myself in the middle of a reading by various faces I recognised from the Volkskrant literary supplement. A bit scary for someone who prefers krimis
De Slegte is for bargain hunters. It has a massive second hand section, making it a brouwser's paradise. A good place to sell your old books, as long as they are very old or very in demand.
For English-language books you have the long-established American Book Center, Waterstones and the English Bookshop. Plus, if we are going second-hand, the Book Exchange.
The American Book Center is more of a portal than a bookshop with a thriving web community. Waterstones only seems to sell three for the price of two books at the moment but if you want to feel at home, most of the staff seem to be Anglo/Dutchies. The English Bookshop says its goes for "good literature not bestsellers" and has a very cosy feel to it.
American Book Center
English Book Shop