Dates back to at least 1551

http://www.oed.com/view/Entry/88227?redirectedFrom=your+honor#eid1534112

With possessive adjective and freq. with capital initial, as Your Honour , etc.: (a) a deferential form of address for any person of higher rank or status (now rare, chiefly regional in later use); (b) a title of respect or form of address for a person holding a particular office, esp. that of court judge.

so i'm guessing it derives from the ancient form of addressing superiors which got applied to english offices, especially the bench but it seems from the OED definitions (more via link) that this concept of honor was widely used and over time got narrowed down.

high quality dictionaries like the OED are really an amazing resource that the internet hasn't been able to quickly and easily replace.

It should be noted that not just Judges are accorded the title. Virtually every elected or higher level government position is accorded the title "Honorable."

That Includes President, VP, Senators, Representatives, Anyone appointed by the President and Confirmed by Congress (So Secretaries, Deputies, Under Secretaries and Directors of the various Agencies) Governors, State Legislators, Mayors, US Attorneys, and US Marshals.

In fact there are many more people who have the title who are not judges then who are.