Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
Media Atelier - Create invoices and estimates on your Mac
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.
Crater - Free Open-Source Invoice app for freelancers & small businesses.
FreshBooks - The ideal accounting software for small business owners.