There are several good independent bookstores in Hobart:
90 - 92 Liverpool Street
They specialise in Sci-Fi, Fantasy, Horror and Crime. Upstairs is Area 52, which is the best place to find comics in Hobart, plus they have a bunch of board and table-top gaming stuff.
140 Collins Street
These guys have mostly literary fiction, non-fiction, Tasmaniana and the like. There's a mezzanine level with a nice little café upstairs.
The Hobart Bookshop
22 Salamanca Square
http://www.hobartbookshop.com.au/ (but it looks broken at present)
I'm less familiar with the contents of this one, but they seem to have a good mix of general and non-fiction, as well as an interesting collection of second-hand books.
138 Collins Street
This is a particularly quirky but good second hand bookstore buried in a little arcade near Fullers. You can't see them from the street. You can find all sorts of things in there, though unless you have hours to explore you may be better off just asking! about 10 years ago