I've had two mainly over the last 10 years. The furthest its gotten was character designs, but the story/plot is all in my head and known only to me. But to give a summary for anyone interested:
One was an idea for a double film entitled "Lost" (this was long before the series ever came out), with the second being "Found". It's basically a futuristic story about a boy who witnesses his mother and sister being murdered, becomes very distraught and a troubled youth, ends up in Juvy and spends all his time in the library there reading (he is actually a genius and just expands his knowledge). He escapes at 15 with a scheme to repay mankind for his losses as he no longer cares for humanity after everything he has witnessed. He secretly creates a cyber/nano human "army" that start attacking cities with bombs (I won't go into the full details of funding and whatnot), creating mass destruction and panic. In the end he is caught and killed by the lead detective/police character.
The "sequel" is mainly a reflection on the way the world/mankind had become lost in its ways (hence the title of the first film), closing with the revelation that the teenage boy had planned on being killed by the cop, as he had experimented on himself with a nano failsafe implanted within his body to set off a signal to go off 10 years after his heartbeat ending (Age 25 was the idea of the pinnacle age for a human to him). This signal was relayed to nuclear devices spread throughout the world in major cities which only he knew about.
To sum up, his death brings about the destruction/end of the world (the only way to be found after being lost, by having everything end).
My second idea was just for an animated futuristic series of a hero/ninja using cybernetic/advanced technologies to bring about justice in a totalitarian/one world power future.