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Calibre

It is the leading ebook management tool. However, you should be aware when you do add a title into Calibre it will embed a bookmark file in the META-INF folder and will modify your .opf file. Other than that it is avaiable for all environments:

Calibre for Windows; 64-bit
Calibre for Mac
Linux; How to install on Ubunutu:

sudo add-apt-repository ppa:n-muench/calibre
sudo apt-get update
sudo apt-get install calibre
Portability on a thumb drive

Adobe Digital Editions

Free and from Adobe. Be advised there has been some issues lately in viewing DRM .epub 3.0 ebooks and the fonts not rendering correctly. This is a bug that was introduced a few months ago on the update but no word yet on when the issue will be addressed. Download page for Adobe Digital Editions. You can install ADE on Ubuntu but you will need Wine. Good article read: "Howto install Adobe Digital Editions on Ubuntu 12.04 and use it with an e-book reader"

BookONO

A management tool I haven't tested or used but they are trying to compete with Calibre so it could be a worthy alternative: BookONO E-book Manager

Adobe PDF Reader

You mention ebooks but not what type. So just throwing Adobe PDF Reader for web .pdfs. Good write up over at AskUbuntu on installing adobe PDF reader on Ubuntu: "How do I install Adobe Acrobat Reader?"

A few others I've heard but haven't used:

Delicious Library 3
Alfa Ebooks Manager
Moon+ Reader
All my books
Data Crow
Lucidor

After the added tag mac-os:

iBooks
KooBits
Scida


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