I'm assuming a lot of people have noticed that with GoDaddy servers, it's very difficult to install Ioncube because of a recent change with their servers running PHP5.
If you haven't signed up with GoDaddy yet, be sure when choosing a shared server, pick Linux and PHP5.
If you run PHP5 on your server, you're going to notice that editing your php.ini file does nothing and will not get the Ioncube loaders to work. Well, here's a tutorial to get Ioncube working!
http://www.geodesicsolutions.com/coblog/Before reading your tutorial, delete php.ini and php5.ini files in your root folder of your ftp server and also delete any Ioncube files and folders you uploaded to start fresh.
I'm so glad I found this guide, it took me 3 hours to figure it out but I got it working. Just follow that tutorial step by step from fresh, and they even have a Ioncube GoDaddy "package" available to download to give you the exact files you need to get it working.
Good luck!