KSP kerbal puppet can be found in Skunk storage bay on some landing pads
There is special tracker mine, stationed inside toroid asteroid in FO. It plays music upon activation and show cat image on explosion.
Inside the Albion Skunk a poster of an iconic X3: Albion Prelude image is visible on one of the walls of the crew quarters. There are other such posters around the quarters of various different old Egosoft games as well.
You can sometime spot the flying saucer, if you get too close, it will speed up to shake you.