Zuora - Zuora creates cloud-based software on a subscription basis that enables any company in any industry to successfully launch, manage, and transform into a subscription business.
Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
Stripe - Online payment processing for internet businesses. Stripe is a suite of payment APIs that powers commerce for online businesses of all sizes. Use Stripe’s payment platform to accept and process payments online for easy-to-use commerce solutions.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
360 Subscription Billing - Automate Recurring and Subscription Billing in NetSuite
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.