You've gotten some great responses so far, but I would leave you with a few other things to think about. Most of the time that I spend with my reader is spent reading it. This makes screen clarity and ergonomics most important to me. The Sony and the Kindle both have the same screen, so that's not a factor. However, given that I might turn the page 1000+ times in the book, ease of page turning is really important. Only you can decide how you would hold the device, and therefore, what would work best for you. Personally, I have arthritis in my hands and find the touchscreen of the Sony much easier for page turns than the buttons of the Kindle.
Next most important, to me, is how well the books are organized on the reader. Sony does a nice job of this with its collections, and an add-on called PRS + also allows for folders. Combined with Calibre, I am able to easily load books and have them organized appropriately. I've heard that the Kindle 3 also supports collections, but am not familiar with how well they work. I've never once missed having wireless or 3G available to me and love having a touchscreen. As you can see from some of the responses, other people want nothing to do with touchscreens and love their wireless. It's personal preference that you have to work out for yourself.
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