Here's a trick you can use to change the flag icon used in Apple Mail. To start, you'll need a new icon. The new icon should be 16x16 pixels in size, and it must be saved in the .tiff format. If you want to change the header icon for the flag column, you can do that too. The same restrictions apply to the size and format of the image.

Once you have your images open a Finder window and go to: Applications > Mail. Right-click on Mail and select Show Package Contents. This will open up a new Finder window.

In the new Finder window go to Contents > Resources. In there you will find files called flagged.tiff and flagged_header.tiff. You can replace one or both of these images with your new image.

Close the Finder windows and restart Mail and your new icons will show up for flagged mails. Before you replace the existing images, you may want to rename them or move them someplace safe in case something goes wrong and you want to revert to the original flag images in Mail.