In the Back to the Future trilogy, the DeLorean time machine's LED readouts display the destination time in red, the present time in green, and the last time departed in yellow. This is a nod to red, green, and yellow being used on the time display in the 1960 version of The Time Machine.
Julian Comstock: A Story of 22nd-Century America. The Narrator finds the novel in an archive maintained by the theocracy for forbidden books of the Secular Ancestors.
The Outside: In The Fallen, it's explained that the word "Morlock" came from an Old Human folk tale, which used it to refer to humans who preyed on other humans, before the Gods repurposed it to describe Their enemies.
Animaniacs: The Pinky and the Brain segment "When Mice Ruled the Earth" opens with a scene H. G. Wells finishing writing this book in 1895. As it turns out, Wells had secretly invented a real Time Machine, which the mice hijack in order to create an alternate timeline where mice are the dominant species.
In "A Clone of My Own", Professor Farnsworth has a time machine similar to the 1960 movie, which he never finished.
In "The Late Phillip Fry", the Professor's forward time machine has controls similar to those of the 1960 movie. When they get to the year 5 Million, they find Expies of the Eloi and Morlocks.
