good question.
I also scrub them real good with 1 part bleech and 2 parts warm water. Scrub them real good with a scouring pad. Next, I always put them inside my oven and bake them for 20 mins at 450 degrees. Flip them over after the initial 20 mins and bake the other side for the same length of time. Of course this only works with rocks small enough to fit inside a standard kitchen oven. The heat from the oven will take care of any micro-organisms and harmful bacteria.
Just be very careful when baking the rocks. Two things, First make sure you watch the rocks. You do not want to leave them in the oven for too long because they have the potential to crack or explode. The heat from the oven will heat up any water trapped inside the rock and could cause them to crack. Secondly, the rocks will be very hot. Use gloves when turning them and also when taking them out. After both sides are baked I let them cool down at room temperature and then rinse with luke warm water. Obviously wait until they are cooled before you put them into the tank, especially if you already have fish in the tank.