I picked up the term from a TV show awhile back, and somehow never discarded it. It's akin to calling it his "stuff" or his "package."

All three terms refers to the whole genital unit, not just the penis. I suppose junk sounds like a negative term, but it's usually used more neutrally, as in "I need to unload all of my junk out of the car," or "I hate unpacking my junk after getting home from a trip." That is an American usage of the word junk, in general; using it to mean "my stuff that I own and need but that I'm not bragging about."

Maybe I'll switch to "package" instead. It's certainly more positive.