Installing IonCube in cPanel
To install IonCube loading in cPanel, run the following as root:
# /scripts/phpext
You can then check if ionCube was installed by running:
# php -v
PHP 5.2.9 (cli) (built: May 21 2009 11:27:40)
Copyright (c) 1997-2009 The PHP Group
Zend Engine v2.2.0, Copyright (c) 1998-2008 Zend Technologies
with eAccelerator v0.9.5.3, Copyright (c) 2004-2006 eAccelerator, by eAccelerator
with the ionCube PHP Loader v3.1.34, Copyright (c) 2002-2009, by ionCube Ltd., and
with Zend Extension Manager v1.2.2, Copyright (c) 2003-2007, by Zend Technologies
You should see a line that contains, “with the ionCube PHP Loader”.
Contact MNX Solutions today if you need assistance with any Linux or UNIX based issue, or ongoing managed Linux services.

This helped me get my website up and running thanks.
Thanks for the post, I needed this installed on our server so that we could install a Magento Extension. Helped save me time trying to figure things out and not bring the site down.