As previous posters have noted (e.g. DoTheBartman), and as a very accessible Futurama trivia site (http://www.imdb.com/title/tt0149460/trivia
) agrees, the "J" in both Philip J. Fry and Hubert (and Cubert) J. Farnsworth are tips of the hat to Jay Ward, Rocky and Bullwinkle creator.
Indeed, in these days of overall lame animation, an homage or two to the genius of Jay Ward and friends is welcome. Especially as Futurama is better (sacrilege though it may be) than Rocky & Bullwinkle, though in the same spirit.
But ... though it's a strong hint, it's not proof that Fry or Farnsworth's middle name is "Jay". The middle name is an open question, possibly resolvable when (if) Fry and Leela marry (again).