ABC Books and BMV books are the ones that most folks know about.
Acadia Book Store sells art and rare books and is located at 232 Queen Street East.
Balfour Books on College Street, near Markham
Circus Books and Music at 866 Danforth Avenue and Jones.
Advertises a 10% discount for cyclists.
Dencan Books and Magazines can be found at 3113 Dundas Street West.
Doug Miller Books is located on Bloor Street West near Manning Avenue.
My favourite little store is Eliot's Bookshop on Yonge Street, just north of Wellesley.
Then there is Pandemonium Books in the Junction at 2920 DundasStreet West.
Seeker's is another favourite of mine @ 509 Bloor Street West, underneath Kilgour's.
She Said Boom has two locations in the city:
393 Roncesvalles and 372 College
Then there is Ten Editions Book Store on the northwest corner of Spadina and Sussex.
These are the ones that I know about, and have visited.
There may be more, so I will add any new ones at some time.