I will admit, when making a fanwork, making references and nods to prior official Trek is seemingly an unavoidable and necessary evil. Even in my upcoming project, I end up paraphrasing a couple of lines or adapting a variation of a micro-occurrence for the story.
Even before I started dipping my toe in to the fan film/tribute film making pool (which sometimes can be a very cold sensation) I never really found such nods and winks to be "fanboyish".
Yes, it would be great to be able to pen a script/story and shoot a fan work without boldly falling back on where we've gone before, but sometimes, under the right circumstances, it helps to give an idea of just when a specific fan work may take place. It also helps for those viewers who may have only just recently gotten into Star Trek to get more of a feel for the wide universe into which they've stepped.
Starting from Star Trek the Motion Picture, forward, it's a little easier for the more expereienced Trek follower to know just when a story takes place, because the stardates start falling into a sense of order, rather than in TOS where the stardates seemed random.
When it comes to a tv series, be it loaded with stand-alones, (TOS/TAS/TNG--for the most part), or if they have broader story arcs (latter TNG, DS9, VOY, ENT) the producers have neither the time, nor the inclination to get new viewers up to speed on the entirety of the Trek universe (same for any sci-fi or fantasy property with a rich and broad background). (That said, I have a feeling that when Star Wars VII: The Force Awakens comes out, it is going to be chock full of winks and nods and gentle hand holding exercises, beyond just the inclusion of the Millennium Falcon, and Han, Luke, and Leia....granted, some 30 years have passed since ROTJ.)
With fan works, one can afford to guide those fresh to the Trek experience with some references to prior official Trek. As long as they don't get carried away.
It's one thing to have a viewer say: "Ohhhhh....I see what you did there," having witnessed a nice, subtle nod to the official Trek. It's another when one goes overboard with the nostalgic references, and a viewer might be inclined to respond with something less charitable like: "Ok, enough with the winks and nods already! Write something original, dammit!"
I do know that that was the case for many when it came to STID.... and admittedly, for all of two minutes, even I felt as they did, but I got over it like Wolverine with a flesh wound. (But I digest.)
I'd say, don't be afraid to dip your foot into the Hot Tub Time Machine for Star Trek.....just don't hang on everything establised previously to sell your own story. Call upon the past when you must, but make sure your story stands well enough on its own.
Take this for what its worth, and with as much salt as necessary.
