One character discovered that he was actually two characters with very similar names and identities who had been fused together by a magical accident. This character tended to change from one to the other at times, with changes in equipment, proficiencies, and ability scores occuring with these changes. Eventually the character split into two separate characters on different adventures.
One character discovered that his father was not a human who had left his mother alone to raise him, but a god who had visited his mother and sired him at that time. Certainly Zeus had plenty of half-human children, and there are other gods known to have had such descendants.
One character discovered that he was related to several other characters who had been involved in the game. The player eventually traced a family tree which connected all of his RPG characters together.
One character had a famous ancestor who had been allied with the now immortal grandfather of assassins in a war centuries before. He was able to use that alliance as a basis for negotiations with the assassins guild. Similarly, characters could find their ancestors were allied with powerful lords, important temples, other guilds, governments, or business powers.
There was a lost magic item, an artifact, which according to lost prophecies could only be recovered by someone descended from the ancestor of a particular character. This character's family had marked all of their children with a tattoo, identifying them as descendants of that man, but had forgotten the reason for it. A prophetic purpose could attach to any character, and could work itself out during adventures, but will be more interesting if it has a hook which will interest the character in pursuing the fulfillment of the prophesy.
One character learned that she had been magically morphed into a half-elf, and was actually a human. We once joked about the character who would discover that before he was this he was that, but before he was that he was another thing, and before the other thing, something else; but this is a real possibility for a mystery option.
An amnesiac character discovered that before becoming a kensai he was a shukenja, and could still use shukenja spells. If a character has amnesia, almost any previous class may be chosen (even barbarian), and the referee may determine that the character forgot everything a long time ago and started over with this new class, or that the character had changed classes, but recently lost his memory.
In an amnesiac character, the cause of the amnesia is almost always one of the mysteries. Various magical, supernatural, or psionic accidents may be the cause, which may lead to many adventures and discoveries. On the other hand, the character might have been hit on the head. If so, the assailant might have been seeking to kill this character specifically, or the character might have been merely a random victim.
One character, a half-breed, discovered that his birth mother had swapped him for a human baby; this enabled him to be a samurai and not be either oriental or human. Of course, he grew up believing himself to be an oriental human, unaware that his racial abilities (such as infravision) were not normal for humans. Half-orcs are the best candidates for this, but half-elves could be similarly treated, especially if the child is being swapped into a wealthy or powerful family. Similarly, irda could be swapped, especially for Krynn elves; and elves for irda. Of course, a character could have been adopted or just found and taken into a family, but never told; this is complicated if his parents have since died.
Two characters of opposing alignments and very different backgrounds discovered they were cousins. One had been from a branch of the family which had broken off, shunned for becoming Yakuza; and then the character had been shunned by that branch of the family for breaking with the oriental traditions by becoming a thief.
Woly Bah'dein was the descendant of Aladdin, and was unaware that his family had the respect and support of a djinni. His surname was given by the referee, and unknown to the player or the character meant "son of Aladdin". Other real or mythic characters could provide such ancestry.
A god had sent one character to protect another, but both were unaware of this. This kind of linked mystery option creates other possibilities--why did the god want to protect the one character, and what right did he have to send the other?
A character was a wanted criminal, with a bounty hunter pursuing him. He had not committed the crime, but had been accused of having done so in a place he had passed through on his way to the city where his adventuring career began.
A character found a gem in a stream, included in his equipment at the beginning of the game, which was a magic item enabling several psionic skills when properly used. The referee can add magical or significant items to the character's equipment, or can add magical properties or significance to equipment the character purchases or otherwise acquires. This is especially useful for those who receive some items from their parents, such as in oriental birthright rolls. However, a character who buys a sword could have unknowingly purchased one which is magical and intelligent, and which has been trying to get back to the family which forged it so as to be restored to its former glory and ability.
There could be an ancient curse on a character's family, which is activated by time or events, which can be undone by some discoverable means. Any set of facts which will eventually cause a character to want to go on an adventure for other than cash will help push the game forward at some point.
A character could have latent inherited psionic powers, activated by crisis situations, which he cannot control and doesn't know about. Thus telepathic, telekinetic, clairsentient, precognitive, or teleportive effects could suddenly occur, surprising the party and helping them in some difficulty, without any of them knowing what happened. The PH has many psionic skills, but there are more in the second edition volume on psionics (and even more in the Multiverser game system which could easily be incorporated into the D&D game if desired).
One of the character's ancestors has banished a demon or other major immortal creature, who is now able to return and wishes to take vengeance on the family of his enemy. Even without mystery options, I've always maintained that the Deck of Many Things is created by an evil supernatural creature as a trap to catch someone against whom he has a grudge--and that the character who draws the void or the donjon is the character the deity, demon, or devil intended to catch.
The character has a child somewhere. If the character is male, he could be unaware that he fathered a child, hidden from him by the mother, or merely unknown before he left. If the character is female, the child was put up for adoption, or the mother was told the child died when in fact it was taken away for some other reason. This also opens possibilities for a mystery option related to the child's other parent.
The character hears a voice giving him advice on situations, which unknown to him is that of a supernatural creature who has taken an interest in his progress and wishes to have him become powerful enough to undertake some particular venture in the future. The referee would tell the player what the voice says, and would provide reasonably reliable (but not always complete) information about circumstances; eventually, the other shoe would drop when the supernatural creature requests payback in the form of a quest. It may be that the quest requires specific abilities or characteristics of the character, such as that it must be a half-elf bard, or fighter with mountaineering skills; or it could be that the quest can only be accomplished by a member of the character's family.
A character's family is involved in a secret society, such as the ninja (if appropriate) or other organization created for the purpose. I have created a number of secret societies, and have put these on the web at my other D&D web site. These include Moradin's Army, the Ring of Blood, the Elfin Legal Defense, the Mithril Chain, and others--and the DM is invited and encouraged to use these and to create his own inspired by these.
The character has an affinity for an unknown weapon, such that if he ever picks up such a weapon he will use it slightly better than any weapon with which he is proficient (an additional +1 to hit), and he will be treated as a specialist if he trains in the weapon once he discovers it. The referee may choose the weapon in secret before the character starts, or may make this one of the mystery options when the character grabs an unfamiliar weapon during a crisis in an adventure.
The character has forgotten a familiarity with a non-weapon proficiency learned as a very young child--such as horsemanship,rope use, boating, swimming, or mountaineering. The referee should assume that the character learned these things while visiting relatives many years before, who have since died and been forgotten by him. It is possible that several such skills might be discovered, related to a particular life style connected to a forgotten corner of childhood. When the circumstance arises, the character will discover that he already knows how to do things he didn't know he had learned.
The character is not from this world, but is a character from another RPG such as Star Frontiers, Gamma World, Boot Hill, or Multiverser, who accidentally landed here and lost his memory in the accident. Once this is discovered, the character may remember where he left certain equipment which is technologically advanced but might be used in the D&D world. He might also find he has skills from that past which he can remember and use.
The character is the player, who fell into the game world and lost his memory. Once he realizes this, his knowledge of the rules of the game might be used to help him in the world. He might also be able to use his own scientific knowledge to develop new things in this world. However, the DM should remember that the reality in D&D is different from that in our world. The four-element alchemy of our ancestors is the reality in that world, and many of our chemistry rules will not apply.
I hope these ideas give you a good start, and that you can come up with many more like--and unlike--these.
The site which inspired this site....
The best new role playing game....
A consideration of time travel....
Other writings by the author....
For your added enlightenment....