I use MapleRead. It allows you to make custom sets of books, add tags, and acts like a server to send books to other devices if you want.
Most important to me, though, is that it also gives you significantly more control of the display. The amount of words books lets you fit on a page at the densest is silly low. MapleRead lets me adjust past the optimal size and down to "actually too small" on both iPad and iPhone. I do most of my reading on a dedicated ereader because e-Ink is a huge difference compared to an LED or OLED display, but when I do have to read on a regular device it makes it a lot less painful to fit more than 10 words on a page.