Ebooks.com allows you to download both epub and PDF with the same purchase if both are available, so I'll preferably buy from them if a PDF is available. That's becoming more and more rare, though.
With a good coupon price, I buy from Kobo. At least recently, this has been most of my books.
If prices are nearly the same, I buy from B&N (I prefer B&N, but I end up buying more from Kobo based on price).
If an ebook is available at Parable (a Christian bookstore), then I'll buy it there because a local brick-and-mortar Parable store gets a cut if I use their link.
I've bought a few books from Sony, but it's quite rare that they have a better price than both Kobo and B&N.
I used to buy occasionally from Christianbook because books published by Thomas Nelson were DRM-free, but that doesn't seem to be the case anymore.
I'll buy from Amazon if a book isn't available as a PDF or epub and I still want it badly enough.
I won't buy from Google because they sometimes make formatting changes to epub books and there's no real way of knowing beforehand if they have or not.
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