I generally do not judge a book by its cover, although pretty covers do tend to pique my interest. If I judged a book by its cover, I would have never picked up my first Kresley Cole book, A Hunger Like No Other, and that would be a travesty! And you especially shouldn't judge the cover of an independent author's book - some author's just don't have the means to create a big publishing house-style cover. Here are a couple of covers that I didn't particularly like, but I loved the books!
The cover for A Hunger Like No Other is not one of the best I've seen! Seriously - every time I look at "Lachlain's" hands...ewwwww! Gross! Eternal Kiss of Darkness, in my opinion, is also terrible. Mencheres is one of my favorite of Frost's vampire boys, yet looks creepy and not nearly as hot as I imagined on the book's cover.
Now, there are books with covers that I loved, as well as loved the actual story. Here are a few examples of covers I like that had great stories to match.
I am a huge fan of Karen Marie Moning's Fever series, and the cover for Shadowfever fit the story and the series perfectly. Kim Harrison's Ever After, in my opinion, was one of the best for her Rachel Morgan series. And really, any cover for a Cassandra Clare book is a winner. I could have used any of the covers from The Mortal Instruments or The Infernal Devices interchangeably.