Be careful what you wish for.
What about someone whose wishes are always granted - this does not mean that he gets what he wants, but that he gets what he said. Whenever he says "I wish....", the universe makes things happen, but the intent is always twisted somehow. Don't screw him over all the time or all the way (like you'd do to someone who utters a wish spell without thinking first), but make things interesting, and let it always have consequences (a bit like Bruce Almighty)
Alternately, he grants other people's wishes the same way. Being a genie and not knowing it would be one secret power...
Another idea is stolen straight from the FR novel Azure Bonds and follow-up novels SPOILERS AHEAD!!!
In the novel, a woman called Alias of Westgate would wake up in the bedchamber of a tavern. She had no recollection of the previous two days, and gaps in the memories of the last year or so, and also didn't know how she got there. She also had some blue tattoos on her arms. She found out weird things over the next couple of weeks, especially while trying to find out how she got these obviously magical tattoos: She suddenly could not drink nearly as much as she used to, she was sometimes controlled by these tattoos - when she had dispel magic or identify cast on them, she'd attack the caster; when she heard someone mimicking the voice of King Azoun, she would attack him.
More disturbing still, when she visits places from her memory, they'd be different from how she remembered. That was mostly subtle things, but she did notice it. Also, people she remembered to have known well didn't remember her.
As it turns out, she wasn't what she thought she'd be: Instead of being a woman in her early thirties, she was a magical creation (think living construct) only a couple of days old. A number of dark forces (including Moander the Darkbringer) had her created and infused with these tattoos, which they used to controll her.
She later gained freedom by eliminating her "parents" - whenever one of these people/creatures was destroyed, one of the azure tattoos would go away. She even met her "father", the Nameless Bard who is now known as Finder Wyvernspur, and has since ascended to godhood after destroying Moander and taking his divine power.
You could do something similar. Make one character a (living) construct, but one that looks and feels like a human, at least from the outside. Give him/her a couple of superhuman powers and some compulsions, a set of false memories to find out about, and so on.
A different concept, but similar to the above: Let one character think he's human, but in truth he's Elan (the psionically created aberration race from the Expanded Psionics Handbook). He was human once, but that was before some cabal of powerful psionicists, wilders, erudites and the like captured him and used him for their experiments for creating a superior race. Give him a gap of maybe 3 months, and some knowledge and abilities he doesn't know how he got them. Let him think he's a fighter or something, when in truth he's a psychic (your choice of psychic warrior, psion or wilder) who can activate several psionic powers - but doesn't know it. When in dangerous or stressful situations, he'll activate them subconsciously to defend himself, and in time, he could find out about his powers and new nature (or corruption thereof).
