When it comes to customization, WHMCS does this well. Whether you want to adjust the look and feel of your billing area (template, theme), make a simple adjustment to how things are handled, or add some complicated functionality, WHMCS can likely be modified to fit what you need.
We’ve been working with WHMCS since 2007 and have developed a number of addons and customizations to WHMCS. Some have been released publicly, some for private customers. If you need something done, please do let us know and we’ll work with you to get your project done.