One of the highlights of the iPad, for me, is reading comic books. I used to enjoy Comics Reader Mobi, but like Camera+, they got caught doing something sneaky by the app review team, and banned from the app store. Unlike Camera+, they never got back in. When their 1-year suspension began to look like a lifetime ban, and since I don't jailbreak, I've moved on to a similar program that is capable of updates, Comic Zeal. It's not perfect, but it's still pretty great. The two caveats (for me) are all the fiddling around with sorting digital comics (I don't think this is an area where I desire skeuomorphism... If, indeed, I ever do.) and having to convert everything.
Unlike CRMobi, Comic Zeal converts all of your .cbr and .cbz files into .cbi files, and then into folders of images on your iPad.
An Update: As I've learned from the developer, this is merely the step of unpacking the zip or rar files to speed loading times. However, the problem remains: How to move your already unpacked or converted or just Comic Zeal-friendly bundle of comics?
When I swapped iPads recently, I did make a backup of my old device, but I opted to treat the new one as brand new. AND, I don't save .cbi files. I make them, transfer them, and delete them. So how to get your comics library from one iPad to the other without rebuilding the world?
I copied my entire 'Imported Comics' folder to my laptop via iTunes. If you have a full backup of your ipad, you can either juggle backups (backup new device, restore old backup, get files, restore new backup), or use a backup-unpacking software, like perhaps JuicePhone (which I have not tried). If your backup is encrypted, then you're probably looking at yet another intermediate step. (edit: All this is assuming your comics are actually included in backups. I don't know if this is the case.)
I installed and ran Comic Zeal on the new iPad to create the folders and database files it expects, so I could see where they go.
I used iExplorer to navigate to iPad -> Apps -> Comic Zeal -> Documents -> Imported Comics
I moved all the files from my backup - whole folders + comic_database.sqlite into the Imported Comics folder on the iPad (I don't know if it used, needed, or threw away the database file. I didn't experiment since it worked on the first try.) Note: I recommend doing this in small chunks. I have almost 10GB of comics data, which took a couple hours to transfer, and somehow this action quickly generated 30-40GB of swap files on the laptop.
I forced Comic Zeal to quit and relaunched it, and there were my comics. In delightfully high resolution.
Excelsior!