Creator Tim Kring has been speaking at the Edinburgh TV Festival, and he let slip a few details about season 3 of Heroes. Apparently, "Volume III: Villains" will last 13 episodes and be immediately followed by "Volume IV: Fugitives", which will run for 12 episodes.
Make of that what you will, but it suggests characters will be on the run from authority figures of some kind. I'd like to think the world will be made aware of super-powered people, and force the "specials" underground, a la X-Men.
Kring also mentioned that, if the writers' strike hadn't forced the premature end of season 2, the second half of season 2 would have been called "Volume III: Exodus". He also mentioned fans won't learn anything more about Kaitlin (Peter's Irish girlfriend, last seen ditched in a "possible future"), we will see more of Echo deMille (the postman with sound manipulation abilities, originated in the recent webisodes), and plans are afoot for invisible man Claude to return (once scheduling conflicts with Christopher Ecclestone have been sorted out). Update: Digital Spy have the video of Kring confirming the above here.
Heroes' third season premieres 22 September on NBC.