Which app should I use for reading e-books on the ipad?

There's other e-reader apps like Kindle and Nook, but then you're limited to books only from Amazon's Kindle book store, or Barnes & Noble's books store, respectively. Basically, books you buy within each e-Reader app belongs to that app, and are not readable by other apps. This means that you won't be able to read your books from iBooks with a different e-reader app. Compared to other e-reader apps, iBooks has the largest selection of books to choose from, so that's your best bet. Plus it lets you upload .pdfs and ePUBs from your computer into it.
If there's some book you can't get on the iBooks bookstore but is available on Amazon, then by all means, install Kindle to read that book. But keep in mind that it'll only be readable by the Kindle app. Make sense?