My manga workflow goes like this: Batoto > Manga Crazy > Kindle Comic Converter > A simple python script to merge the cbz files into one big file > Kobo external memory
This is the script if you are interested:
http://paste.muratcansimsek.com/disofigudo Others are all apps you can easily find. I use OS X, but they are all multi-platform.
I recommend Kobo Glo or Kobo Aura H2O for manga. With the new Kobo Glo HD and the Kindles you might have problems. They have no SD card support and I believe Kindles have margins with comics, but I am not sure.