the cake is a nod to the phrase "let them eat cake" by the elite (when revolutions happen they give something back to the peasants to calm them down, that something is referred to as the cake)
think of it this way
glados is the daughter of the elite who inherited all the wealth and is tasked with running aperture science and apertures goal is total domination of the planet through technology
chell is a criminal (whose fighting the system of the elites) who gets caught and is sent to aperture science to be tested on as a prisoner
when chell rebels and nearly wins glados offers cake to trick her
the scientist learned about the true purpose of the company and is warning everyone that the cake (whatever glados offers) is a lie and she should not be trusted
the scientist guy is the equivalent of the conspiracy theorists of the real world who no one believes
do the math on why valve expected this to become a meme

>>728905535
Cube <3