I'm not so sure that there is a great one yet.
Currently, I'm using Book Bazaar Reader which is a Modern (nee Metro,...) app that is available free from the Microsoft Store. It's quite functional but not full of a lot of customization features. It works very well in a purely touch environment.
I've used calibre's ebook-viewer and found it functional, but since it's a Desktop application it has its functionality issues in a pure touch environment. Recent updates have improved things, but I found it marginal without a pointing device or a software simulation such as TouchMousePointer (highly recommended as a useful tool for general use). I've also used Kindle for PC (the Desktop version not the Modern App that is preinstalled on many Win8.1 devices) and, again, found it less than great in a touch environment.
I keep calibre on my tablet (Dell Venue 8 Pro 32gb + 32gb microSD) as an ebook manager/converter and export (Save to Disk in calibre terms) my reader. I keep very few books in my reader's library, only those currently being read. Once finished, I delete them, retaining only the copy in the calibre library which is on my expansion card.
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