One of the weaknesses of the Amazon Kindle is the inability to read books on anything other than a Kindle or iPhone/iPod touch. That will be changing soon though as Microsoft showed off an Amazon Kindle reader on Windows PCs at the Windows 7 launch event. I still think the B&N Nook beats the Kindle for a number of reasons, but this is one less advantage the Nook has over the Kindle.
Dedicated ebook reading devices can't be beat in terms of reading and impact on your eyes, but reading on a PC can also be a good experience due to the backlighting, presence of a Windows PC, and cross platform access. The beta for the Kindle for PC software will roll out in November and I am signed up to try it out since I still have Kindle content I purchased and read on my iPhone 3GS.