The Congress set mostly in a collective hallucination that looks like a trippy '30s cartoon, has Tom Cruise showing up in his Maverick attire, or at least someone using his likeness as their toon avatar.
In the Broad City episode "Twaining Day," Abbi wants to train Shania Twain. She says, "Let me train her with you. I could be your Goose!" Trey says, "Do not bring up Top Gun right now." The reference works, though, and Trey lets her help.
Saints Row: The Third turns Boss, Laura Bailey!Boss in particular, into a fan of the film: half the voice samples will reference the movie in one mission while she will make numerous comments about it.
Wing Commander famously centered on a pilot known as Maverick, with Iceman being one of his squadmates. However, in this case, "Maverick" is lampshaded as being an Ironic Nickname for the cool-headed by the book pilot. His wingman Maniac is another matter entirely...
Three stations in Splatoon 2: Octo Expansion are named after Top Gun characters: Maverick Station, Goose Station, and Iceman Station. Fittingly, all three stations involve piloting an Inkjet in order to reach the goal. Furthermore, the subtitles of the three missions are "Revvin' up your Inkjet...", "Listen to its howlin' roar", and "Jet into the danger zone..." — all referencing the lyrics to Danger Zone, which featured in the film's soundtrack.
Archer's Catchphrase is "Danger Zone", and both the song and film itself are frequently mentioned. Kenny Loggins also did an Adam Westing appearance in the episode "Baby Shower" and did a country-music cover of the song.