Kerbol
None known
Moho
There are large, steep vertical "tunnels" that could be considered easter eggs, and anomalous forces are present around the rim of each tunnel.
Eve
None known
Gilly
0 degrees, 0 degrees, there is a perfect square pyramid.
Kerbin
Five Monoliths
Inland Kerbal Space Center
Memorial to the Mk1 Command Pod
A temple in the desert - Underground as of v0.22
A crashed flying saucer on northern ice cap
Scorched Mk1 Command Pod, Liquid fuel tank and LV-T45 rocket in a hangar on the Insular Airfield
At the exact north pole, there is perfect square pyramid which flips Kerbals randomly. This is not really an easter egg, but is a product of glitches in terrain mapping.
Mun
Three monoliths
Three mun Arches
Neil Armstrong Memorial
Crashed Flying Saucer
Minmus
One floating monolith
Duna
Giant Kerbal face
The camera which looks like that of the Curiosity rover, buried in the soil (appears to be underground, as of at least 0.19.1)
Hill making SSTV signal (source of signal now several hundred meters beneath hill as of 0.22)
Ike
Magic Boulder - There is a monolith on the boulder. Boulder contains strange clipping boundaries that can result in your ship exploding seemingly spontaneously. It also seems to glow green as if it is radioactive.
Dres
None known
Jool
None known
Laythe
None known
Vall
Stonehenge formation in the southern hemisphere
Tylo
Crater with Carl Sagan's face
Cave-like underground formation
Bop
Dead Deep Space Kraken
Pol
None known
Eeloo
None known.
Overall
While not easter eggs per se, the exact geographical poles of most bodies have highly unusual topography, usually making them inaccessible.
IVA
Some of the cockpits have post-it notes and other humorous writings inside them. The writing is somewhat blurry and hard to read, but still legible. For transcripts of the notes, see the respective part pages.
Parts
On the Z-100 and Z-400 Rechargable Battery, the logo claims the batteries are Batt Man Batteries. This is a reference to Batman.
On the Communotron 88-88 is the hexadecimal number 0x62656570. When 0x62656570 is converted to ASCII it spells "beep".
Also on the Communotron 88-88, is the serial number 04101957, which is the launch date of Sputnik 1, 4th of October, 1957.
Loading Screen
While not that much of an Easter Egg instead of a reference, the loading screen makes a reference to The Hitchhiker's Guide To The Galaxy, stating "Answering Ultimate Question" one of the well known phrases from the book.
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