As for PDFs, I have recently looked up reviews of PDF handling for both the PRS-650 and the Kindle 3. The Sony PRS-650 seems to me to handle PDFs quite a bit better than the Kindle.
Here is a review for the 350 (I couldn't find the review for the 650, for some reason):
http://www.youtube.com/watch?v=jE6Iv...r_profilepage#!
Here is a review for the Kindle 3's PDF rendering capabilities:
http://www.youtube.com/watch?v=zlZ9c...r_profilepage#!