I got this question quite a lot and I have to say it's quite a good one. Because I live in the Netherlands I'm kinda limited on where I buy my books. I mainly read English books and normal bookstores actually don't sell them over here.
Here I have a list of websites and bookstores where I buy most of my English or Dutch books:
Bol.com is a Dutch website where you can basically get anything, you can compare it to Amazon.com. over the years I have bought many things there, from make-up to perfumes and books. Books are however pretty expensive on bol.com, around 2 to 4 euros more expensive than for example thebookdepository.com, which brings us to number 2!
I have to say this is my most used website for buying books. Around 80% of the books I own I have bought on this website. They have a really good customer service and the good thing is you can pay with paypal, which is great for when not having a credit card. paperbacks cost around 6,7,8 euros a piece, which I find a great price! hardcovers are more expensive. They cost around 16,17 euros a piece. When buying hardcovers I always compare bol.com and thebookdepository.com, sometimes bol.com has hardcovers which are little cheaper :) When having problems with your order it is easy to mail the customer service at thebookdepository.com, they reply to answers very fast and when something is wrong or if your order hasn't been delivered they just give you back your money!
In our village we have 1 shop called Bruna. They sell magazines, pens, things for your printer and books as well. Bruna has tons of stores across the Netherlands. Our Bruna sells paperback books and sometimes hardcovers as well. Most paperbacks vary from 10-20 euros, this because they have been translated to Dutch. Dutch books or translated books always are more expensive than the English ones. Our Bruna also has a section of German books, which I find great. The area I live in is very popular among German tourists, so that's why this shop sells also German books. I never bought a German book in there but I'm planning on doing soon.
I go to Brussels several times a year (I live close to the Belgian border). Brussels has a waterstones shop which is pretty huge and they sell tons of English books over there. Every time I visit brussels I make sure to have some time to stop by :)
Betterworldbooks is one of my favorite websites to buy books on. They only sell 2nd hand books and they ship them to Europe for free! The money they get for the books go to literacy funds and high schools to support libraries. In the past I've had some pretty good deals on there. At least once a month I check if they have new books added to their YA section and when I found one I like I also buy them straight away. Their prices vary on the condition and the popularity of the book. And now comes the bonus point for them : You can pay with PayPal as well!
These were the places I buy most of my books. Sometimes I wish that I could support independent bookshops more, but the stupid thing is we don't have any close to where I live. I also really want to buy books on amazon, but because I have no credit card I can't :(
Where do you buy your books mostly?