This Official Site article reports that JJ and his agent are discussing a new deal. If this happens, his club option for 2007 will be eliminated and a new multi-year contract will take its place.
As the article states, he had the third lowest run support in the Majors. He definitely would have been in consideration for the Cy Young had he a few more wins. But can he repeat his 2006 season again? Rox Girl has expressed doubts about that, questioning whether or not he was pitching over his head for most of the season.
And as malakian noted, Justin Hampson is a Padre now and Mike Venafro and Nate Field were outrighted to the Springs. The 40-man roster now stands at 37. King, Martin and Mesa will all becoming off (though one or two may be back).