In the clock room look at the books underneath the table for references to existing award-winning books by Stephen Hawking, Robert Heinlein, Martin Heidegger and Madeleine L'Engle.
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Egg id: 388
In Dr. Brain's office, look at the notes on the board to find one stating "Help little girl find lost dog". This could very well be a reference to Pepper's Adventures in Time where Pepper's dog Lockjaw is kidnapped by General Pugh's daughter Ima.
Even though Pepper's Adventures in Time was released shortly after Castle of Dr. Brain, it was likely in full production at the time.
In the Star Room, one of the alien planets is described as "Metallica exports heavy metal bands.", referring to the famous heavy metal band by the same name.
