1)
Gabriel Knight 3 included a few secret societies in its storyline, with varying levels of relevancy to the story, and did so very well, I would say. (Since the societies in question might be seen as a spoiler, I'm taking a cue from a thread on spoiler tags and using a source block in place of one)
Scroll down for the societies that I recall being included:......If I recall correctly, the Rosacrucians, Priory of Scion and at least onesociety created for the story (although that might have been tied into oneof the other societies; it has been a while since last I played the game).The Knights Templar may have been mentioned; I'm not sure, I'm afraid.2)
The Broken Sword series featured the Knights Templar in at least its third and I believe first games (I haven't yet played the first, but its subtitle rather gives this point away, I would say ;)). Again, since it has been a fair while since last I played it, I'm not sure about the fourth game.
I'm not sure whether the society involved is one that you might be interested in (yet again, I haven't played it in a while, I'm afraid ^^; ), but Fahrenheit (a.k.a. Indigo Prophecy) also involved secret societies, as I recall.
