I am looking at the flow from source (online, email inbox, personal documents, Gutenberg.org and gutenberg.net.au ) to Kindle; and from Kindle to colleagues (sharing the whole file, or sharing excerpts); and from Kindle back to PC for editing (correction, adding, repurposing to blog or wiki or email).
Kindle can natively display, search and annotate PDF, TXT and the Kindle format (azw, azw1, mobi, prc). The working principle is to minimize steps between getting the content and using it, so the materials of these filetypes are most convenient. But of them, TXT may be best since it displays well, allows the above Kindle tools and later can be copied, moved or edited on computer. By contrast, PDF and AZW is less readily edited on computer.
The option of converting (the free service via email to one's kindle account) from DOC, RTF or HTML is good when you need to preserve hotlinks, images, and formatting. But for text-centric materials, it seems that TXT is the best coin of the realm for easy circulation between Web, computer and Kindle, and back again.