Specifically for toilet bowls, if you find that a stain won’t shift even after using a normal toilet bowl cleaner solution and a normal toilet brush, don’t try to brush harder as this will scratch the porcelain surface. Also don’t try something abrasive like steel wool or the green/blue side of a kitchen sponge.

Instead, what you want to do is dissolve the stain. Others have suggested CLR and that might work. But if not, then you can obtain “acidic toilet bowl cleaner”, which contains hydrochloric acid, aka muriatic acid. This will remove most anything normally staining a toilet bowl, but make sure you handle it sturdily and carefully. Gloves and eye protection are highly recommendes, until the bowl is brushed, the stain is gone, and the bowl is flushed. Turn on the bathroom fan or open a window for ventilation.