Calibre is such a big suite for organize bookshelves, too much software for simple one-by-one book reading.
Amazon Kindle is great, book reading experience syncronized through all your devices. Nice annotation functionality and many other features but only books from Amazon Kindle Store are allowed.
Sony Reader. It’s my choice. It lets me add my own epub books, good highlight and note features, there is a funcitonality to export annotations. Download Reader
Adobe Digital Editions, incipient software
EPUBreader add-on for Firefox, lack of UX work