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There is a big thread discussing the pros and cons of the various readers, you'll find it with a search if you're interested.

But for me Comic Zeal is by far the best, and they add regular improvements.
 
ComicZeal seconded...

just got my iPad last week, have a couple thousand cbr and cbz files loaded up already. ComicZeal is fast and easy and great. i also used the iPhone version for a long time.
 
I've been using ARCreader and generally like it. It works well, but I'd like some better file management...folders, grouping or something.

Gonna look at Cloudreader and Comicbook lover tonight. (Comiczeal looks good, but I'd rather not have a pay program if a free works better)
 
I stumbled on a program in the AppShopper app, Bookman.

It's great so far. It has shelfs...and multiple ones...for organizing. Has both tap and slide page advancements.

So far, it's the best free cbr/cbz app I've found.
 
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