I've bought many e-books over the years at the Pragmatic Bookshelf.
One neat feature I haven't noticed till today is that now they can deliver your e-books to your Kindle with wi-fi.
It's a small touch, but downloading the e-book (not only the first time, but on every update), getting your Kindle, connecting it, finding the file and moving it to the proper folder and ejecting it from the computer is a lot more work than you have when buying from Amazon (i.e.: click on the link and wait a few seconds for the download).
With this, it's exactly the same process after the purchase (it's still much easier to buy in Amazon).
Given their great selection, it's well worth checking them out!