A great and very comprehensive tool, which allows you to do almost everything to manage you software development company. From managing a project's portfolio, predicting the future to tracking people's work and managing your finances.
Hub Planner - Transparent Resource Scheduling, Timesheets, Vacation, Resource Requesting, Project Management & powerful Reports in an agile designed, feasible & intuitive software for simple planning
Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.
10000ft - 10,000ft's high-level project management software helps teams get the clarity and insight they need to look ahead, avoid pitfalls, and plan for growth.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
ResourceGuru - The fast, simple way to schedule people, equipment, and other resources 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.