As the question says really. The application is on a local Windows 7 machine.
I'm looking for a free application that can do this sort of thing. It should either time when the window is in focus or when the application is running. Thanks.
Depending on your situation, this could be overkill. I find AutoIt and similar programs are useful for tasks like this.
To expand on Garet's answer:
Depending on how the programs you are looking to restrict are built, you have a few options with AutoIt. Look specifically at the functions WinWaitActive, WinGetProcess, WinClose, WinKill, ProcessClose, TimerInit, TimerDiff, Sleep.
A combination of these will let you see when a specific window opens, time how long it is open, and kill it when it reaches a certain point in time. They will also let you continue to kill it anytime it opens until another specified time period is exhausted.