I use 2 iPads for that.
And on a single iPad, 2 different e-reader apps serve the purpose just as well. The quality of the secondary e-reader app isn't all that important, as it's usually only needed for reference purposes. I currently need to do this with a book that has many end-notes but the publisher was sloppy/amateurish enough to fail to hyperlink them.
So, I read the book in Marvin, and the end-notes are open in Stanza. Sometimes, though, it's useful to see both the main text and the end-note at the same time, and for this, I prefer using 2 iPads simultaneously, with the same book open in Marvin on both iPads: main text on iPad 3, end-notes on iPad 1. This is not as crazy or extravagant as it might seem -- in fact, it's pretty standard in modern work environments to have 2 displays connected to your computer.
Another instance where I find this very useful is when I try to read a book in the original language, but need to keep a translated version open for reference/help purposes. Switching back and forth between both books on the same iPad all the time, would be annoying and inefficient. And we probably can never expect the iPad to allow for a split screen, in order to display 2 books at the same time. Here again, 2 iPads are ideal to handle this need.
I'm looking forward to getting a Retina-screen iPad mini, so that it can replace my iPad 1 as my secondary/reference iPad. I prefer reading on a 10-inch tablet, but for consultation/reference purposes, 10 inches seems like overkill -- 7 or 8 inches would be ideal. At the same time, I'm not willing to pay the very high price of $330 for a non-Retina iPad mini, so I have to wait for now.