It's always nice to have a few well-trained assassins around. Set a newbie assassin on a rebel stack (preferably in your neighbor's province, to avoid devastation), and kill the captain. Lather, rinse, repeat.

I usually don't go after faction family members. You can have fun with assassins by annoying your neighbors with sabotage. But they are also great at clearing out the hordes of diplomats wandering your territories. After you lose a city or army to a bribing diplomat, it's cathartic to cut a path through the old geezers hanging around.