There are alternatives available for the WHMCS. Best alternative is Blest, HostBill. Blesta is not open source while HostBill is the opensource. Blesta used to run only on Linux platform while HostBill used to run on Linux as well as Windows platform. HostBill is very convenient for the large web hosting companies.
I have to be honest here, there is just no competition for WHMCS. The amount of third-party add-ons and themes makes it clearly better.
You also have to consider how much people are used to the WHMCS design when making a purchase or using the interface after purchase.
There are several available like HostBill, Blesta, Clientexe, BoxBilling etc. which mainly supports Linux platform. They support common features like Invoice & Payments, Product Provisioning, Client Area, Marketing etc. and 2 of them are Open Source namely BoxBilling and Blesta.
While there some alternatives that supports Windows like Blesta, Clientexec, Atomia etc. From my recommendation its better to opt for the billing script which is easy to implement and provides maximum compatibility.
WHMCS is one of the most popular choice for billing platform. Although there are lots of options out there but the completeness that you can get in WHMCS is just so hard to pass. Blesta is the next best option for me followed by Billmanager.
I am not one to support a monopoly, but WHMCS is the only pre-existing web hosting billing solution available in it's class. There is simply not another product that competes at the same level. Considering how inexpensive it is for what you get, it is a good deal.
cant afford whmcs go with a reseller plan from host 9 or something they give out free whmcs license along with package you better off going that way. I personally wouldnt trust free software for private data such as your clients information.