Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
Ledger-cli.org - Ledger is a powerful, double-entry accounting system that is accessed from the UNIX command-line.
Free Invoicing Software - Free Invoicing Software provides the facility of online billing.
FreshBooks - The ideal accounting software for small business owners.