Derek Flack's blogTO list might be best taken as an indicative list rather than a master one. It's still quite a good reference.
The list continues for another thirty entries. It's quite worth reading.
Toronto book stores haven't all packed up shop just yet. On the contrary, a survey of the city's book scene reveals that bricks and mortar shops are still plentiful despite the near-constant doom and gloom we hear related to online sales. In fact, the local book shops that have been the most resilient in the face of competition are independent outfits with a specific focus.
These are the top book stores in Toronto by type.
Academic Books
The Bob Miller Book Room is tucked away in the basement of a building near Bloor and Avenue Rd. but grad students will know it as a place to find academic trade paperbacks that you can't your hands on anywhere else. If you like literary theory and history, a visit here is a must.
African and Caribbean Literature
A Different Booklist is a cross-genre bookstore with a focus on literature and history related to Toronto's African and Caribbean communities, but it's more than that too. Here you'll find an excellent selection of books for youth, texts on international politics, and human rights.
Architecture and design
For coffee table worthy design and architecture books, look no further than Swipe Books at 401 Richmond. Owner David Michaelides is passionate about books and stocks his store with hard-to-find titles that you won't see on shelves elsewhere. The magazine stock is also pro.
The list continues for another thirty entries. It's quite worth reading.