What's the best way to calculate time passed since last playing app?

Basically to do a Farmville crop growing over time type system.

I would guess save the system time in a PlayerPref on minimize and then check it when you run next?

Any other suggestions or can anyone point me at the functions to do that?

PlayerPrefs are only stored on the players computer. Is would be better to store information at a server.

Take a look at the wiki: Server Side Highscores

Good starting point with SQL, PHP and JS code.