Probably one of the more / most stupid terms coined in this century...Black Eyed Peas sang about "...all that junk in your trunk",even more moronic...somebody thought it was "contemporary Chic"...seemed to be popular with the black teens that I worked with in Los Angeles
I personally think that the term "junk" refers to all of a guys gear. The penis, the sack, the balls, there's a lot going on down there. And it just sits there like a pile of junk, because it's usually just in the way. That's my take on it.
The first time I heard it was in the movie that the dude from Saved by the Bell was in... Mark Paul Gossalear, or whatever. It was something about college. Anyway, the one frat dude told the other dude to "kick me in the junk", so since then, I've often called my nuts and dick my "junk". It's just easy to sum it up by calling it my junk. For example, I got kicked in my own nuts and dick by a dude, and it was just easier to say I got kicked in the junk.