I have a PRS-650, and I agree that it's PDF handling is a step up compared to the Nook and Kindle eInk devices, but there are compromises on ALL the eInk devices when it comes to PDFs, the Sonys included.
PDFs are designed to be rendered at a fixed page size, usually one much larger than the small screen available on compact eInk devices, and there is just no easy way to shrink them down for display on a smaller screen without messing up the formatting.
My PRS-650 is ok for plain text, which is reflowed reasonably well, but the placement of figures or formatting of tables gets mangled pretty badly if you try to reflow them.
As has been said, the Sony does use the official Adobe Mobile PDF reader, so as long as you set the font to 'S' (which is the Sony's way of disabling reflow) everything will look absolutely perfect, and it will stay that way as long as you only use ZOOM to make it larger, and stay away from turning on reflow by using the larger font sizes (switching to a larger font will activate reflow, which is fine for simple documents, but not for complex formatting, which is better handled by using ZOOM).
One nice thing about the Sony's ZOOM feature that does help a little though, is that you can just use your finger to drag the image around while it is zoomed using the touch screen.
The only hassle about using ZOOM is that you can only view a single page ZOOMed at one time, and working your way through a large document this way can be very tedious.
I have a small 10 inch Netbook PC with both Win7 and Ubuntu 10.04 loaded, and I use that for any PDFs who's formatting makes them difficult on my Sony.
I paid just $199 for my PRS-650 and about $220 for the Netbook, so altogether I still have less invested than most folks spend on an iPad or other high end tablet. I suppose someone might ask why not just spend a little more and get a iPad that can 'do it all'?.
Will the iPad let me read for a week or more without recharging and fit in a hip pouch like my Sony? Does it run both Ubuntu and Win7 giving me access to 99% of the serious applications on the planet like my Netbook?
The simple answer is that, for the kinds of things I am interested in, the combination of my PRS-650 and Netbook works about 500 times better than an iPad, and with freeware, and overdrive, virtually all of my software and books are free.
The Netbook is only about the size of a medium sized hardback book, and it packs a lot of power into that small package. It's great to be able to run full blown version of Adobe Reader and ADE, plus the full versions of applications like Office and Open Office.
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