I occasionally fill mine with water and a drop of bleach and leave overnight. It doesn't seem to do the nappies any harm and it gets rid of the smell.
MY OH, who was always very anti cloth, has been properly turning his nose up at the pampers we have had to use this week because DS has been poorly! He moans that they stink and when he took one off earlier he said 'what am I supposed to do with this?' A convert