PrefersNonDefaultGPU=true makes laptops/computers with multiple GPUs prefer to launch the application with the most powerful GPU available by default when launched through the icon.
Currently this key is used in games such as SuperTuxCart and presumably others.
The option allows users to use their dGPU without having to worry about setting environmental variables etc.
Currently in order to run the game on the discrete GPU with recent versions of GNOME the user has to right-click the icon and then press the "Launch using Dedicated Graphics Card" button, using this patch however no other actions are required rather than just clicking the game's icon.
Also on GNOME, once the key is set a user can choose to run the game on the integrated GPU by following the same procedure used to run to run the game on the discrete GPU.
That is, if a user on a laptop wants to save battery using the iGPU he can easily do so.
For reference purposes:
DesktopEntryKeys specification
Discussion by the specification's authors
Useful reading