What are they?
Alma-2 describes these works to his son Helaman as he commands him regarding the records in Alma 37. From this passage, we learn that these "secret works of darkness" include "oaths," "covenants," "agreements in their secret abominations," as well as "signs" and "wonders."
In Helaman 10:3, we learn that these secret works are associated with "murderings, plunderings, and all manner of iniquities."
Where do they come from?
Both Jacob and Mormon make it clear these works are ancient, though in very different ways. Jacob accomplishes this by teaching us who authored them in the first place: "the father of lies...that being who beguiled our first parents, who transformeth himself nigh unto an angel of light, and stirreth up the children of men unto secret combinations of murder and all manner of secret works of darkness." (2 Nephi 9:9)
In 3 Nephi 3:9, Mormon quotes the leader of the Gadianton robbers, Giddianhi, in which he makes this assertion: "I am the governor of this the secret society of Gadianton; which society and the works thereof I know to be good; and they are of ancient date and they have been handed down unto us."
Are they among us now?
Sadly, Moroni teaches us that the Book of Mormon would come forth "in a day when the blood of saints shall cry unto the Lord, because of secret combinations and the works of darkness." (Mormon 8:27)
Nephi prophesies that these things will be among us at the same time he reveals their author:
22 And there are also secret combinations, even as in times of old, according to the combinations of the devil, for he is the founder of all these things; yea, the founder of murder, and works of darkness; (2 Nephi 26)
What becomes of those who participate in secret works?
This should come as no surprise...things don't end well for those who engage in secret works:
15 Wherefore, for this cause, that my covenants may be fulfilled which I have made unto the children of men, that I will do unto them while they are in the flesh, I must needs destroy the secret works of darkness, and of murders, and of abominations. (2 Nephi 10)
25 I will bring forth out of darkness unto light all their secret works and their abominations; and except they repent I will destroy them from off the face of the earth; and I will bring to light all their secrets and abominations, unto every nation that shall hereafter possess the land. (Alma 37)
9 And behold, that great city Jacobugath, which was inhabited by the people of king Jacob, have I caused to be burned with fire because of their sins and their wickedness, which was above all the wickedness of the whole earth, because of their secret murders and combinations; for it was they that did destroy the peace of my people and the government of the land; therefore I did cause them to be burned, to destroy them from before my face, that the blood of the prophets and the saints should not come up unto me any more against them. (3 Nephi 9)