In all fairness I must say that some of my favorite books, like A Tale of Two Cities by Charles Dickens and One Hundred Years of Solitude by Gabriel Garcia Marquez do not have the most interesting covers I have ever seen, but are literary masterpieces none the less.
Some books, even if they were mediocre, I will keep because of their cover designs. I have compiled a couple of my favorites here. These are, for the most part, great novels as well. I did not include any of my art books because that is a whole other realm of discussion.
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Extremely Loud and Incredibly Close by Jonathan Safran Foer
Everything is Illuminated by Jonathan Safran Foer
The Brief Wondrous Life of Oscar Wao by Junot Diaz
Leaf Storm and Other Stories by Gabriel Garcia Marquez
In the Woods by Tana French
Innocent Erendira and Other Stories by Gabriel Garcia Marquez
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The Three Musketeers by Alexandre Dumas
The Girl Who Played with Fire by Stieg Larsson
The Idiot by Fyodor Dostoevsky
Half Life by Shelley Jackson
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On a side note, all the books in this series by Stieg Larsson (The Girl with the Dragon Tattoo, The Girl Who Played with Fire and the upcoming The Girl Who Kicked the Hornet's Nest, are excellent. I would highly recommend reading them.