What do you think Johnny’s last words to Ponyboy mean?

The last words that Johnny says to Ponyboy are the last words that he ever says:

Stay gold, Ponyboy. Stay gold

Johnny's words refer back to the poem that Ponyboy recited while they were hiding out in the old church. The poem is "Nothing Gold Can Stay" by Robert Frost. The basic idea is that good things don't last forever. Nature is full of beautiful things, but because nature is dynamic and seasonal, those beautiful things eventually turn into something less beautiful.
Nature's first green is gold,Her hardest hue to hold.Her early leaf's a flower; But only so an hour.Then leaf subsides to leaf,So Eden sank to grief,So dawn goes down to dayNothing gold can stay. 
Johnny is trying to tell Ponyboy to stay innocent and pure. He knows that Ponyboy is smart and has great potential to do something beyond the gang life. Johnny doesn't want Ponyboy's only experience at being gold to be now. He wants Ponyboy to always be that way. Johnny knows that if Ponyboy becomes hardened and bitter like Dally and the other Greasers, he won't be as great and beautiful of a human being as he currently is: Ponyboy won't be golden anymore.