The best part of Calibre is that it makes it easy to export your ebooks to your ereading devices: Kindles, Sony Readers, iPhones, and Android phones are all supported, and you can apparently access your books from the internet, too. You can transfer files easily from PDFs to .epub to whatever format you need, you can send RSS feeds and magazine articand it also supports comic formats like .cbr and .cbz, too.
I'm sure there will be some glitches along the way, but I'm in a serious honeymoon period with Calibre right now. It's elegant, simple, and non-proprietary.