Best apps I've used from a library organization standpoint are Marvin (iPad only for now but the developer said iPhone version is targeted for August/September release) and Mantano Reader (Android). Before Marvin, it was Stanza. Handled the 3,800 epubs I have loaded without any slowdowns on the iPhone 4.
Needless to say, nothing beats Calibre on the desktop.
Edited by rui-no-onna - 8/19/13 at 6:56am