I was going to add my favorite billing software, but there are so many threads where everyone posts their version of 'the best billing software', I thought it best to comment on the subject in general.
Commercial versus Free or GPL'd:
While commercial scripts offer trouble free installation and operation, it's very difficult to customize the code (I'm not referring to look) for any one specific purpose. Although many are written for both hosting and domain registration, some are written with domain registration as a primary purpose, while others are written for hosting.
GPL scripts are generally more difficult to install and have a few more bugs, but they may be customized more readily. More are written with hosting as a primary purpose, but may offer domain registration functions.
Before you can decide on a billing system, you must know which control panel you'll be using if you plan to have automated account creation (in general this is a bad idea due to fraud) and if domain registration is needed, which registrar you'll be using.
Will you be selling other products or services?
Do you need multiple administrator logins?
I don't think you want to go too "cheap" when it comes to your billing software. The price WHMCS charges for their application is VERY reasonable for what you get. Plus there's a huge community of people in their forums should you need help, and lots of people recommending the software.
I don't use it myself, as my business is different. But from the amount of times I've heard recommendations for it, AND from my personal dealings with Matt (owner of WHMCS), I would definitely recommend WHMCS.
Rob Moore - Founder/President DemoWolf.com - Video Tutorials for hosting companies, since 2005