phpCoin is still free if you don't go over 10 sites. Their new fee structure is outlined here:
Personally, I think they deserve to be paid. It's a solid script. First time I used phpCoin it only worked with WHM/Cpanel and did a great job. I think there's a Plesk mod available now.
If you don't mind a reasonable license fee, Whois.Cart() deserves consideration. This script works with several host APIs and domain registrar APIs, and it's a full-blown billing system. It's more sophisticated than phpCoin but will probably require more of your attention. Setting it up is easy, skinning it for your site is where you'll likely spend most of your time. http://whoiscart.net