I use Bookman (
http://itunes.apple.com/us/app/pdf-c...436673025?mt=8) and love it. You have the option of either using it's built-in FTP server to transfer files to it, or use the "Open in" functionality, or of course use iTunes to transfer. I tend to use
File Browser to browse my media share and grab stuff. I use the FTP function for more files at once. I like the organization; it lets you create folders and open them up without having to view the whole library at once (rather like iBooks).
If I had to change one thing, occasionally it doesn't handle two page spreads as well as I'd like - not sure if that's because of how the CBZ file is packed or labelled or what.