MAVProxy is a open source minimalist and plugin-based GCS for Mavlink based autopilots (such as the APM). Until recently, it was only able to run on Linux systems. It has since been updated by Tridge and myself to include full compatibility for Windows systems.
MAVProxy can be found at https://github.com/tridge/MAVProxy and an installation and user's guide is available at http://www.qgroundcontrol.org/mavlink/mavproxy_startpage.
And the obligatory screenshot of MAVProxy running in Windows and Linux at the same time (above)