The “Mohole” is a hole located at the north pole of Moho. When the game first came out, it was caused by a terrain glitch, although anomalous forces around it would cause vehicles to accelerate toward it. Eventually, it was given its own dedicated biome and became a permanent part of the game.
On Vall, there is a stone formation at that resembles Stonehenge.
You can find a crashed UFO on the northern ice cap of Kerbin. There is also one on the Mun.
The “Nye Island” station might be a reference to Bill Nye.
If you destroy a level 3 Astronaut Complex, you’ll be able to see a toilet in the rubble.
There is a temple/pyramid located on Kerbin. If you crash into it, you will see that its name is Tut-Un Jeb-Ahn.
If you go to the Mun, you can find a memorial to astronaut Neil Armstrong, the first man to walk on the moon, who died in 2012.
On Duna, there is a giant Kerbal face in the sand. This is most likely a reference to the “Face on Mars,” a hill on Mars that resembles a face in certain images.
The “Sagan Sea” biome on Laythe might be a reference to scientist and author Carl Sagan.
Numerous assembly parts include short references.
The loading screen sometimes says “Answering Ultimate Question,” a reference to The Hitchhiker’s Guide to the Galaxy. The price of the EAS-4 Strut Connector, 42, might also be another reference.
The loading screen sometimes says “Falling With Style,” a reference to Toy Story, where Woody says Buzz is only “falling with style” instead of flying.