I use Comicglass. Just transfer the cbr files to the App in itunes.
Here's a tip if you are on a mac: You can transfer an entire folder of comics, but first you have to rename the folder by adding a .pkg to the end of it. (You will need to confirm you really want to do that). That will trick the system into thinking it is a package file, and then you can easily transfer an entire folder. To see what is in the package, or modify the contents on your mac just right click or cmmand click it and do show package contents.
I have over 11GB of comics on my new iPad and am loving it!