jkOnTheRun has this comparison today. He looks at iBooks, Kindle, Zinio, Comixology and Newsstand. Barnes & Noble doesn’t have a retina-enabled ereading app yet.
Here’s what he has to say about Comixology;
The iPad really got me back into reading comics, and Comixology quickly became my go-to source for digital comics. The new iPad really makes this a fantastic reading experience. With older iPads, the text would be fuzzy enough to force me to use the pane-by-pane view. With the new iPad, I don’t need to. While the issues look great as they are, Comixology is stepping up their game by updating (for free) most of their library to what they call CMX HD. At the time of publishing, roughly 1,000 titles have been upgraded. When you are shopping for comics it will say CMX HD in the lower right hand corner of the page if it is available in HD. This was the app I was most looking forward to on the new iPad, and it has not disappointed me at all.