I have iBooks, Kindle, Kobo, B&N and Stanza. I prefer iBooks.
Kobo drives me nuts because while it does tell me how many pages I have left in a chapter, it doesn't tell me how many I have left in the book. While I like knowing how far I have left to go in a chapter, I'd rather know how far till the end of the bpok, if it has to be one or the other. But sometimes I buy a book from Kobo--sometimes they offer a much better deal on a book I want. One day I'm going to get off my lazy keister and look up how to de-DRM them so I can read them in iBooks.
...which is what I do with Kindle books. I only have the Kindle reader on the iPad for checking out samples and downloading purchased books to the iPad just long enough to put them on my computer for de-DRMing.
I should probably delete B&N--I tried it with a free book and didn't find anything special about it.
Which leaves Stanza, which has some advantages over iBooks--and iBooks has some advantages over it. It's ultimately a wash, and iBooks ends up getting used just because I've already imported all my books to it.