I have heard about Calibre for some time, but i just installed it (Thanks to Eric Hameleers for providing this package in Slackware) and feel the power of this application. It handles my ebook perfectly, because it can download the metadata about the book from the Internet. I can see reviews/ratings from other users collected at Amazon or any other online book store. This way, i can see whether this book is good enough to read.
If you have other devices, you can export the PDFs you have to the format used in your device. Calibre also provide on the fly connectivity by using Stanza for iOS-based devices. I can read my collection at my desktop via my iPad. That means i don't have to waste my free space on my iPad and i can use it for other apps or files.
This application is updated every week and it was developed by a guy name Kovid Goyal since 2009. Right now, it has been used in over 200 countries around the world, a real proof that this application deserves to be selected as the tool to manage your digital files.