Windows: There are some great multi-monitor management tools available but if you're trying to keep things free and open-source the pickings get a little slimmer. Dual Monitor Tools is a collection of open-source applications for managing your multi-monitor setup.
Dual Monitor Tools isn't a single application but a suite of individual apps. Load only the ones you need and conserve memory in the process. The suite currently includes four applications: Swap Screen, Dual Wallpaper, DisMon and Dual Swap.
Swap Screen enables hotkey management of windows across your multiple monitors like moving, minimising and rotating the contents of monitors from one to the other. You can also restrict the mouse movement to a single monitor. Dual Wallpaper is a simple wallpaper manager that offers different wallpaper on each screen or spanning wallpaper. DisMon allows for selective disabling of monitors — handy for gaming and particularly picky applications that don't play nice with multiple monitors. Dual Snap is a screen capture application designed for capturing images from the secondary monitors. As noted above each application stands alone so if you see at tool that interests you, you can pluck it from the suite and use it without the others.
Dual Monitor Tool is open-source, Windows only. For more multi-monitor goodness make sure to check out how to make the most of your multiple monitor setup under Windows 7 and the five best tools for managing your multiple monitor setup.