When Daphne Ashbrook (who played companion Grace in the TV movie) appears, her character immediately decides she wants to shag the Eighth Doctor, with plenty of Refuge in Audacity. A nod to all the controversy over having the Doctor kiss Grace in the first place.
Just like with Ace, Melanie "Mel" Jane Bush's (Sixth and Seventh Doctors) last name was established in other parts of the Doctor Who Expanded Universe.
Lucie calls the Monk "The Meddling Monk", the first time he's ever been officially called that in all of Doctor Who. He has been called that by fans for quite some time.
Trolling Creator: Nicholas Briggs deliberately trolled the fanbase as much as possible in "Dark Eyes", almost diving into the Last Great Time War for just a few minutes before yanking the idea away again.
The Cliff Hanger between Zagreus' first appearance and the subsequent episode lasted a year and a half. Close to the end of that release gap, in the audio "Omega", Zagreus is prominently listed in the credits. It's an in-story actor playing Zagreus on a Gallifrey-themed cruise ship. He has one line.