tinyE: Theres a nice slam at Doom in Duke3D. Plus, I don't know if this counts as an egg, but in the expansion DUKE in OUT in DC, the time machine you use in the secret level is a replica of the time machine in the original "Time Machine" movie with Rod Taylor.
God, I need a life.
Duke 3D is full of easter eggs. Luke Skywalker, Indiana Jones, The monks from Rise of the Triad, The Terminator which had two, Star Trek, Mission Impossible, Beavis & Butthead, it just keeps going and going.
Blood had a mutilated Duke Nukem, and lots of horror references from movies like Friday the 13th, Nightmare on Elm Street, The Shining, and even the Simpsons Treehouse of Horror.
Need to play Shadow Warrior through again, but some that come to mind are Lara Croft, TMNT and the Monty Python killer rabbit.
I beat Redneck Rampage again about a month ago and sadly realized it lacks in the easter eggs :(