In the seventh mission of the game, there is an assassin talking to another about the basics of stealth. The assassin's dialogue is a direct reference to the tutorial from Thief: The Dark Project.
Contributed by ThisGuyInTheSuit
In the H.Q. in one of the shops, on the second floor there is a large oval painted on the wall. On the outside of the same wall you can find a second oval. Reading a note near the first oval reveals a scientist wanted to use these to travel long distances, referencing the Portal series.

The note reads:
The "door to nowhere" has proven to be a safety hazard, but for me this project is an endless source of inspiration. With the proper application of energies, I believe I can transform the door frame into a window of sorts, one that will allow a traveler to cover the distance from my workshop to some distant, arbitrary point in a single step. Currently the step leads to a sheer drop, straight down into the courtyard, but in time it will bridge gaps that will boggle the mind. Such work is many years away, to be sure, but if I survive the plague I'm sure to succeed.
Contributed by Outofmind23
The mission Lady Boyle's Last Party is loosely based off Edgar Allan Poe's story "The Masque of the Red Death".
Contributed by Outofmind23