Check out Microsoft.IoT.Lightning.Providers. To implement pull down "Microsoft.IoT.Lightning" via Nuget (the source is at Microsoft.IoT.Lightning.Providers project). From there follow the usage example in PwmConsumer. It worked well enough to variable speed control a motor.
Here's a code sample that sets the duty cycle to 25%:
LowLevelDevicesController.DefaultProvider = LightningProvider.GetAggregateProvider();
pwmController = (await PwmController.GetControllersAsync(LightningPwmProvider.GetPwmProvider()))[1];
motorPin = pwmController.OpenPin(5);
pwmController.SetDesiredFrequency(50);
motorPin.SetActiveDutyCyclePercentage(.25);
motorPin.Start();
I also put together a blog post on PWM in Windows IoT with in-depth step by step details about how to do this.