It took mine about 3 hours to back up, but I think I know why. I forgot to remove extra copies of "Wired" magazine.
This App is great and the magazines are awesome to read on the iPad, but they really cause problems during backup. The more of them I remove the faster it goes. I try to leave only the current copy on the iPad.
If you have a lot of apps like this with files for it that aren't needed they will really slow the process up. If you want to keep the files see about transferring them to your computer before attempting the backup. It will go a lot faster.
Also backup regularly the more frequently you back up the less has to be done each time as the new backup only does the new info.