Here is a couple ways to hide a water stain on a ceiling.
After the original leak has been fixed. If you do not want to repaint the entire ceiling,try touching it up with a can of Kilz Upshot. This is an aerosol can, ceiling primer that is tinted to more closely match any aged white ceiling.
If you do prefer to redo the entire ceiling try some Sherwin Williams Visible Solutions ceiling paint. It goes on kind of a Violet color and dries to a nice bright White in 20 minutes, which will ensure you that you don'tr miss any spots on your ceiling.