Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
RTG Bills - Billing Made Easy: RTG Bills is software for legal billing and time tracking; for attorneys in law firms and sole practitioners; lawyer billing and accounting software; trust accounting
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
CaseFox - Web-based legal software for law firms and lawyers that has timekeeping, legal billing, expense tracking, time billing, trust accounting, case management, and many more features.
GnuCash - A personal and small-business financial-accounting software, licensed under GNU/GPL and available for Linux, Windows, Mac OS X, BSD, and Solaris.
TekLAW - New Wave Tek, home of TekLaw law office practice management software. Calendaring, billing, case management software.