I have found a great rust/iron stain remover for toilets. It is called Super Iron Out and is a powder which you put into your toilet and you can let it sit for a few minutes then clean the iron away with your toilet brush. The directions say that you can also use it in your dishwasher, water softener, laundry, and tubs. I haven't tried it in those areas yet. The only drawback is that it has a smell when it reacts with the iron so ensure that your bathroom is well ventilated when you use it and do not mix it with any other cleaners!