I usually fill up my laundry tub, add some bleach and soak them for an hour (trading them out as often are needed to process all my pots and usable 6-packs). I don't think bleach gets used up in a few hours.
Then I give them a few tubs of clean water. So far, I've never noticed any problems in germination the following year. And BTW, an aquarium expert told me that 2 ml of HO (hydrogen peroxide) per 25 gallons is really good at killing algae. And since the instructions say you can actually gargle with the stuff, it can't be very harmful. And it is cheap!
