In NYC I usually go to Strands Bookstores to get discounted current books to read and it took me a while to find an equivalent in Stockholm. Finally found a decent place called Bokskotten at the corner of Mäster Samuelsgatan and Regeringsgatan. If you can't find what you're looking for there, Akademibokhandeln is just across the street.
Every now and then, I do go to Stadsmission to see what books they have. It's a secondhand store so don't expect too much of books in English selection but do expect to buy much less than the typical bookstores.
I've been to Hedengrens Bokhandel on Stureplan also. It has a good selection of books in English too but I found it to be a bit pricey.
Bokskotten - http://www.bokskotten.se/
Akademibokhandeln - http://akademibokhandeln.se/
Hedengrens Bokhandel - http://www.hedengrens.se/
Stadsmission - http://www.stadsmissionen.se/