The nice thing is that all three stores/apps let you preview the book, so I was able to make an informed decision. iBooks has a really nice look and interface, with virtual pages that flip realistically, but both iBooks and Nook have mildly obnoxious load times on my 2g iPod Touch, so I bought it for the Kindle reader, which has very quick loading. If I had a more powerful device I'd probably have gone with iBooks. Nook reader was pretty unremarkable, although it was nice that you could totally customize your color scheme. All 3 apps do let you customize your font size and choose from at least a few different color schemes, and all 3 offer a decent sepia-toned scheme, although only iBooks displayed the little grayscale subchapter icons properly against a colored background:
Screenshots, for the heck of it:
(possible book spoilers? Don't look too hard at the words if you haven't read them yet, but these are all from either the prologue of the Book of Atrus or from the beginning of the Book of Ti'ana, I just screencapped the first break icon)
Kindle Reader:
http://puu.sh/gnU
nook reader:
http://puu.sh/gnV
iBooks:
http://puu.sh/gnX
_________________
Now shut up and make it so you only have to jump once. (Spoilers)
Luig'Ahn KI: (need to update)