Hi Bigjohn ! The average layman might have a hard time telling apart man-made and natural, but any gemologist that is half decent can tell the difference. With a ruby, they can tell if it's synthetic by the residual traces of chemicals from the manufacturing process. They can also tell buy the growth curves, synthetic rubies have a more curved growth line. You must see this under a microscope to tell the difference.
With Sapphires it's even more easy, you don't even need a microscope to perform the " breath test " A natural sapphire won't cloud as quickly.
As for heat treated stones, they are also identified easily with the right equipment. I can usually tell without equipment just by looking at the over saturated color. ( I look at way too many stones in my free time
) I have lots of info on this in print from scientific publications, but here is a link to the most reputable site I know : GIA
https://www.gia.edu/gem-treatment
An fake emerald is easily identified under a dichroscope. Also you can usually tell by it's color even without equipment.
Diamonds are a little trickier as the process has improved in making the synthetics, however even these can be identified with a thermal test.
To my knowledge, there is no stone that a certified professional can't identify.