A geek today is quite likely to reference the pop culture of 30 years ago: "Do or do not, there is no try", "Beam me up, Scotty" and "Ground control to Major Tom" are easily and commonly recognisable. (The first is Star Wars, the second is associated with Star Trek though it never appears verbatim, the third is David Bowie's Space oddity.) A geek 100 years from now might be familiar with those quotes, in the same way we are familiar with "Good night, sweet prince", but he is more likely to use references to the pop culture of his day.
Trouble is, of course, that the pop culture of 100 years from now has not yet been written. I can invent it, but then it wouldn't serve the goal of a pop culture reference: such a reference isn't used only to convey an idea between characters, but also to the reader. So it's real-life modern pop-culture I have to reference, if I reference anything - not invented pop-culture.
I can operate on the assumption that some references are timeless, like Shakespeare. It might turn out to be true of some of the references in question, but I doubt it will be true of all. And no less important, even though older references would still be recognisable, they wouldn't be as commonly used, would they?
The geek in the first paragraph is of course just an example - everyone refers to pop culture to some extent. However, being very much a geek myself, I find that such references are much more common in a geeky group, to the extent that writing a geeky character who does not make such references is almost unrealistic. The reference is both a way to convey a larger meaning in a few words, and a way to enjoy the work being referenced, in a way that includes the people having the conversation, and also the geeky reader (the likely reader of a sci-fi novel).
In light of this, how do I avoid references to modern pop culture becoming too jarring for the sci-fi setting? My current novel is set ~100 years into the future.