Zoho Invoice - 100% free online invoicing software for small businesses.
Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
FreshBooks - The ideal accounting software for small business owners.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
QuickBooks Online - QuickBooks Online is a Cloud Accounting for small business that can be used on iPad, mobile phone or computer to do invoicing, billing, run reports, or even pay employees online.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.