FreshBooks - The ideal accounting software for small business owners.
Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
Bill.com - Bill.com provides ACH payments processing, automates your accounts payable and accounts receivable processes.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
AND CO - AND CO helps freelancers, entrepreneurs and other small businesses run their business smarter.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.