For some time Bookshelf had my vote, as it let me read all the Baen Webscription books I'd bought back in my Palm days - with direct access to the Baen site. However, I recently started using Stanza, as the Del Rey free ebook offer included T.A. Pratt's Blood Engines, something marypcb insisted I read, and the Random House servers could be read straight from Stanza.
It turned out to be an easier tool to use than Bookshelf, and less prone to hanging when opening new book sections. It was also far more configurable, so I settled in to switching between two different tools - especially as Staze supported Fictionwise, so I could uninstall eReader.
Today I was able to uninstall Bookshelf - as Webscriptions now supports Stanza. Now I can read all my ebooks in one place - removing another icon from my application list. I've still got one other ebook reader installed, Amazon's Kindle, which I loaded using my US iTunes account. I've still not put any books on it, and at this point I suspect it's there mainly as a curiosity rather than anything useful.
So a few less icons.
That's a good thing, I had too much installed.