The Kindle is a great little machine (and the £89 keyboard-less version is excellent value). If you buy books or newspapers from Amazon they are perfectly formatted for the 6" screen and arrive in the proprietary file format. However, most of us have a stack of PDFs (books, work material etc) that you can drop into the /documents folder on the Kindle, but if they're formatted for A4 printing then you're either looking at very small text or trying to zoom & scroll the display.
k2PDFopt does a very good job or re-flowing the pages of a PDF (keeping diagrams in the correct place) to fit the 6" screen. I haven't yet tried the Windows or Linux versions but the Mac build is a bit fiddly (make sure you read the install instructions!) and you can't be shy of the command line!