iBooks generally has the best UI, also the ability to import ePubs. Syncs with iPhone as well
Kindle- Because i really enjoy amazon, and they have a massive selection of books. Syncs with iPhone
Nook for iOS- I have not bought anything off of this, mostly because i want to keep purchases between iBooks and Kindle. However, i LOVE the "publishers settings" meaning the book is displayed page by page as the original book. Nook has a wonderful sick innerface with features that competes with iBooks , but i invested to much into Kindle to drop it as my secondary e-reader.
In Closing. I use iBooks for all my ePubs and any book i am interested in reading if its in the store. I use Kindle for my past Kindle books, as well as my secondary store for what the iBooks store does not have. I love that we are given choice though. long winded, sorry!