There are 2 places that I used to go to; Kyobo and Samsung downtown. Kyobo use to have a great selection but now they are down to the classics, though they do have a decent Lonely Planet selection (at least the last time i was there). Samsung has some new, popular novels, though the selection is limited and a lot of the books have been made into movies or vice versa.
I dont even bother with shopping for books in daejeon anymore. easier to hop on the bus to seoul's bus station (can't remember the name) and they have tons of books! plus you never have to go into seoul! just get back on your bus when you are done shopping