The cracked version saves are in:
In the above location Program Data is a hidden folder. Make Windows show hidden files to be able to see it.
The original (non-cracked game) saves are in:
C:\Program Files (x86)\Ubisoft\Ubisoft Game Launcher\savegames\[a long series of numbers and letters]\46
The savegames folder is not a hidden folder. Just installing Far Cry 3 does not create it. It does not show up until after you have actually started a game. For sure by the first checkpoint in the game. If you have installed Far Cry 3 on several PCs in your house via Steam using the same login, the game saves in the above 46 folder are transferable between your house PCs. So you can archive various game saves such as the most advanced ones, in order to avoid spending a lot of time to get to the same point on another PC in the house.
You can also save the intermediate game saves too if you want to be able to replay missions. Normally, Far Cry 3 does not allow replaying individual missions once they are completed. You have to start from the beginning to get back to a mission. Archiving is a way to get around this. Archiving is also a good precaution in the event the game crashes and loses game saves. Or if Steam cloud synchronization loses the game saves. Some people prefer to turn off Steam cloud synchronization in settings. So each PC has its own game saves. Useful when multiple people are playing the game.
The cracked-version game saves are in a different format, and are not transferable with the Steam/Ubisoft game saves.