and where they ARE . (So you can go, too.)
http://www.wavebooks.com - Title Wave Books - Anchorage, Alaska
http://www.citylights.com - City Lights Bookstore - San Francisco, California
http://www.strandbooks.com - Strand Bookstore - New York, New York
Bibliomaniacs - Delavan, Wisconsin
http://www.quimbys.com - Quimby's - Chicago, Illinois
What and where are your favorites? Carmichael's Bookstore in Louisville, KY
A Reader's Corner in Louisville, KY
The Dawn Treader in Ann Arbor MI. The BEST used bookstore I have ever seen.
I am totally in love with the two Outland stores in Oslo, and Tanum is great as well.
Tanum is like Norway's biggest bookstore, and Outland is this fantasy/role-playing/anime-manga/sci-fi- whatever place. Nice shops to buy gifts in 
Half-Price Books - Indianapolis, Indiana (3 locations)
The Book Rack - Greenwood, Indiana
All these stores sell books at 50% of the cover price, and the Half-price books stores have a great clearance section (many books for a buck), and have many sales, and coupons throughout the year!!!!!!
the used book cafe--in NYC, Soho. It's a beautiful used book store on Crosby street, b/n prince and houston. the atmosphere is great--it has the typical high ceilings and inside its dark and sheltered feeling. the cafe is run by volunteers...and I think for every book you buy, they donate money to a charity...the housing works project? something like that.
Crossword Bookstore, Pune India.
Popular Book House, Pune India.
Both of them are really good.
The Book Rack -El Paso Tx
Bookmans - Phoenix, Az
both are great used bookstores ^^
I haven't seen a bookstore like this one: http://www.powells.com/
The main store is in Portland, Oregon (fairly close to my hometown, which is a couple hours away). "With three rambling floors covering an entire city block", yes you read that correctly it is an entire city block, and is three stories. It has practically floor to ceiling shelves with new and used books on it side by side. They even have maps when you go in there. There are also pillars in the building which famous authors have signed! You can easily spend hours in this store. I need to go back! Citylights in San Francisco is awesome but the prices are a little big high (Guess the backalley honoring Kerouac has something to do with it 
)
If you're ever going to Frisco, make sure you visit Green Apple Books, is bigger than Citylightsand you can virtually find everything that has been published in english. Second hand or new...
Oh and it has a decent music store too
Check it out
http://www.greenapplebooks.com/cgi-bin/mergatroid/index.html
http://www.greenapplebooks.com/cgi-bin/mergatroid/gallery.html?id=38KCpM36 When I first moved to Brisbane from Mackay, I was really excited to find Borders--three storeys of bookish goodness, with comfy reading seats and in-store toilets and a cafe and everything you'd need to live there except sleeping bags and a shower--given that the only non-secondhand bookstores in Mackay were dinky little Angus & Robertson stores (little one-storey chain stores with a so-so range and shop assistants coming by every five minutes to ask whether they can help you, even if you've told them you're just browsing).
Borders has since become something of a guilty pleasure, thanks to my finding out how things stand in Australian publishing between multinational chains and independent booksellers (poorly, for the independents). My favourite independent bookstore in Brisbane is Pulp Fiction, which specialises in Science Fiction and Mystery titles. It's quite a little shop, but they pack as much into the limited space as possible. The store owners are friendly and have no problem with people coming in and spending hours in the shop, making hopeless gargling "oh god why do I have to be so broke" noises. They also have an excellent understanding of the market--very up-to-date with new releases, author tours, who's in the middle of writing what at the moment, and so on. I've been known to go in just to eavesdrop on them, because it's such a pleasure to listen to people with that depth of knowledge of their business and their genre. They also are very willing to order any title into the shop if they don't have it on the shelves--another nice way of compensating for the limited space--and sometimes will thank you if you can put them onto a title that they hadn't received through their ordering catalogue.
