Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
BillGrid.com - BillGrid is an easy to use online invoicing, billing and expense management system that will save you time with tracking clients projects, expenses, invoices and payments.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
ChargeOver - ChargeOver automates recurring billing, subscription billing, & payment acceptance. A SaaS that integrates with Xero, Quickbooks, & has an API. Free trial.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.
fusebill - Fusebill is the leading recurring billing and subscription management software for businesses. Try Fusebill for subscription billing made easy!