I'm a sucker for those nifty page-turning animations (where it looks just like a real page turning), and I find the Nook Reader and Google Play Book to be the best looking. However, as far as I can tell, I can't sideload my own collection into the Google Book Reader, so I'm sticking with the Nook Reader app.
However...I find that most eBook readers (including the NookReader) only let you arrange books by title, author, or most recent, and I like to arrange my books into collections or series.
Mantano reader lets you tag however you want to put into collections, but it doesn't have that beautiful page-turning animation...
By the way, Mantano is excellent for reading PDFs!
FB Reader is awesome! Using Calibre on the PC, I can edit the metadata to give my books whatever tag I want, and in FBReader, I can organize books by type, series, or just about any other way. It even lets you long-press a map to make it larger (for those of you who are fantasy buffs).
It does have page-turning animation, but not nearly as beautiful as the Nook Reader, so I keep my collection organized in FBReader, and then if I want a book to look really good when I read it, I just copy the file into the Nook Reader documents folder using a file app like EZFile Explorer.
To summarize: Mantano and FBReader for organizing/reading=great. Nook Reader for really Awesome reading!