After some WHMCS related security issues through 2012, a lot of folks have looked into running BoxBilling. Even after cpanel bought out whmcs not long ago vulnerabilities are still popping up and you have to upgrade your whmcs install VERY often which can be a pain. Just like NeoBill or WHMCS, BoxBilling is PHP/MySQL powered and 100% free. You have to sign up with BoxBilling to receive a free license but that's about it. Let us take a further look into BoxBilling vs WHMCs -
There are many payment gateways available for BoxBilling, which is one thing that makes it equally flexible as WHMCS. They both have client and product searching features, but everything is laid out a little differently. To get a real good feel of the differences take a look at their demos at http://www.whmcs.com/demo/ and http://www.boxbilling.com/demo. A lot of people feel that WHMCS is too bloated so boxbilling can be perfect for you if you feel this way.
Dedicated server hosting providers, such as DaCentec, use BoxBilling and I've been with providers who use BoxBilling. I see no major quality difference between BoxBilling, if it's done and configured right, to a WHMCS installation from a clients prospective. From an admin perspective you would have to change up the interfaces a lot to make them similar.
BoxBilling fees can be cheaper for a startup at $5/mo for the pro vresion. WHMCS costs $18.95/mo bare minimum. The pro version is for if you feel like you have outgrown BoxBilling as it allows unlimited everything. With the free boxbilling version you are limited to 1 staff member, 2 product categories, 3 promo codes, and 5 products. This is severely limiting! WHMCS was cheaper in the long run with the Owned licenses but they have done away with that since October of 2016. You can still find some people with owned licenses willing to sell them though.
At some point eventually you might want to migrate to WHMCS if you chose BoxBilling to start with. Be aware you have to purchase conversion scripts from WHMCS or a third party to convert your client list from BoxBilling to WHMCS which can be a pain in the butt. I've requested the conversion scripts before from WHMCS and they wanted upwards of $150 for it. You could probably pay your own developer to create something for you at that fee.
Boxbilling does seem to be missing a few features. Compare the feature lists of BoxBilling vs WHMCs here http://www.boxbilling.com/features and here http://www.whmcs.com/features/. In my opinion BoxBilling was a little harder to use in comparison to WHMCS. Honestly I forgot the exact reason but, BoxBilling was missing a pretty important feature that I needed so, I switched back to WHMCS a few years ago. I think Boxbilling will be fine for a smaller company with fewer clients. WHMCS requires that you pay upwards of $15 a month, every month, while BoxBilling is free. As long as you do not mind putting some effort into maintaining a free web application, BoxBilling will be a great option for you.
In conclusion it is all really up to your preference and goals with your billing system, but we prefer WHMCS. If you've had experiences with either one of the billing systems feel free to leave a comment below and let us know what you thought about BoxBilling vs WHMCs.