I use ClientExec. It's inexpensive, powerful, easy-to use, and has a great team behind it. However, until the new version is released, the staff have too much power (weak ticketing system), and it doesn't integrate with any control panel. However, that also makes it very convenient if you want to use it for a non-hosting related venture.
ClientExec is very slow for releasing updates but the software is very stable and does what it says. There are many lacking features that I find the software almost useless though, you can't email any of your clients all at once or even a certain group...... Not much for intergration, no Enom.. no coupons, no affiliate system.... no auto account creation.
ModernBill, I heard their customer support it terrible but I can't say much not being an owner. This system promises a huge amount of features and intergration with Enom, coupon system, affiliate system and a lot more. Off the shelf it doesn't support recurring paysystems, but I heard there is a custom hack for it. Intergrated ticket system and you can intergrate Kayako support desk..
WHMAutopilot - Quickly becomming the ModernBill replacement with the anticipated V3 version. They're promising a ton of new features and enhancements that should really put it on the map for small to large companies. V3 release is expected near the end of May.