Manage Your E-Books in DEVONthink
Out-of-the-box DEVONthink displays and searches many file formats including PDF or Office documents. For files it doesn't understand it uses Quick Look and Spotlight to make their proprietary content usable. With these two free plugins you can add the .epub file format to your system. As soon as you've installed the plugins, DEVONthink shows at least book covers, finds books by their content, and converts them to plain text.
Unfortunately there seems to be no plugin yet that lets you read the whole book. If there is and I just haven't found it yet let me know.