Also a ComicZeal user. Nice enough plus you don't have to use iTunes to transfer if you are using Wifi at home. It will transfer whatever you drag onto the program itself (started up from the desktop) and send it to you iPad once converted.

One I'm using more often lately is Comicglass. The main differences between it and ComicZeal are server interfaces and loading for offline reading. Comicglass uses MediaServer which lets you browse files, pix and archives directly off of your PC and streams/loads from there. You can chose any image in the archive itself to act as the cover (it has a clone of iBooks for a display if you want a more graphic look), uses subfolders (locking subfolders if you wish). It also has the option to automatically breaks double page images into single pages.

Honestly, both are cheap enough you can't go wrong with either.