In a lot of cases the prices of ebooks are being set by the publisher and not the stores themselves. There was a whole kerfuffle back in the early months of 2010 about this (starting with Amazon actually removing the buy button from the books for one publisher, then blinking and backing off. You can blame Apple, essentially, since Apple and the publishers came up with this pricing model for their launch of the iPad and their ebook store.) Five of the six major publishers have entered into agreements with retailers for an "Agency model" of pricing (these publishers are referred to as the "Agency 5".) With pricing for their ebooks, the price is set by the publisher and the book should be the same price wherever you shop. (The slight discrepancies in listed prices are due to taxes, I believe. Some retailers will add the tax when you checkout, while others include the taxes in the list price.)
I think the publishers wanted to step in and start setting prices before eReading takes off in a big way - it's been growing steadily, but they expect this Christmas to be the year when it really takes off now that there are many eReaders on the market that are affordable. They're hoping to establish a high price point and have these new readers expect ebooks to cost that much.
Kobo actually blogged a bit about this when it was happening. Have a look at the following articles for more information:
Countdown to Agency (and Party Like it’s $9.99!)
HarperCollins and Simon & Schuster and Sales Tax