There are large, steep vertical "tunnels" that could be considered easter eggs, and anomalous forces are present around the rim of each tunnel.
0 degrees, 0 degrees, there is a perfect square pyramid.
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.
Three mun Arches
Neil Armstrong Memorial
Crashed Flying Saucer
One floating monolith
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)
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.
Stonehenge formation in the southern hemisphere
Crater with Carl Sagan's face
Cave-like underground formation
Dead Deep Space Kraken
While not easter eggs per se, the exact geographical poles of most bodies have highly unusual topography, usually making them inaccessible.
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.
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.
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.