To a certain extent it depends on how closely entwined your reference is to the intended appreciation of the story. To take the example of a pop song: if you need to listen to the song to really get the story then I would tend to leave that as an unspoken rule. Make sure people get what the song is so they can track down a copy but there's no need to ram it down their throats.
If it goes even deeper so a reader needs to understand things about the artist and the context in which the song was written, what was going on in the news when it attained its highest chart position and other ephemera surrounding the song production the situation changes. In that case you need to evaluate whether your writing could genuinely be seen as an independent piece of work, or if it is, in essence a "bonus feature" to the thing that you're referencing.
In the first case then the best thing to do is to not really mention it explicitly. If people get it then fine otherwise, as it's an independent work in its own right, also fine. Some people will get a little added wrinkle on what is, no doubt, already a fine piece of work. You should, however, be careful to ensure that other readers don't even really think they've missed anything.
If the latter case then be up front to your audience somehow that this is essentially a commentary upon a specific song and "for psycho fans only" (that's a Tenacious D reference by the way).
As long as you give your audience the information they need then nothing is really "wrong".