Everyone has expected Khan to show up in next year’s Star Trek II, but now it’s pretty much confirmed. TrekMovie managed to get confirmation that Benedict Cumberbatch is in fact playing Khan as everyone expected (I still was hoping for Trelane though…). They do say that the movie will not be a rehash of Space Seed.
They also go on to confirm that Spock Prime will factor into the plot in some way, and other places such as AICN confirmed him as well. TrekMovie also talks about Klingons in the movie.
How all of these elements will fit together will likely remain a mystery until the movie comes out as Abrams is notoriously secretive.