My explorer found a "Ruby" special on the map, and I am unsure what industry this helps? It goes up 40%, but fails to list WHAT it puts up 40%. Odd design decision.

I don't really recall what they do off the top of my head, but I say that if we're speaking about production, Gold seems a logical candidate. At least, more logical than the others.
Of course, it may be it doesn't help an industry, but something else. Medicinal herbs, for example, increase the rate at which your population increases.

if it doesn't say i assume commerce, since gold veins buff gold mines, basically veins in general, but the medicinal herbs i believe do the same, no idea.

Well, I've just discovered a field of sapphires, and they boost commerce, so I guess rubies might do that, too.
By the way, doesn't it say what it does when you right-click on it, either?

Commerce - Rubies, diamonds, sapphire's and etc effect the output of your commerce buildings. Placing a commerce building near these resources increases the output.
Mines - If you find gold, silver, copper or iron then the output of your mines increase. The closer you place a mine to one of theses resources the higher the output.
Medicinal herbs - They increase the number of people immigrating to your colony. Place a church close to the herbs.

Natural Wheat Fields increase Farms, as does placing them on grassland and next to water (river).
The temple of war increases your military, but I can't remember exactly how.
Fountain of youth heals units.

And, for completeness' sake, let's not forget about the various forests (for example redwood), which, of course, boost wood production.

Gems also benefits native gold mines.