In The X-Files Season 10 Episode 02 titled "Founder's Mutation" there are two movies seen being played on the television at different moments. One is in the hospital maternity ward and is a scene from Escape from Planet of the Apes and another is in a dream sequence where Mulder is watching 2001: A Space Odyssey with a fictional William around age 8. The scene from 2001 is at the beginning with the man apes. I couldn't help but notice the similarities between them and wonder what their significance is to the episode.
In season 10 at the hospital it plays a scene on the tv where the female ape is giving birth to baby milo whos name is later on changed to "caesar". In this film ceasars parents pass on to ceasar the idea that humans are not bad. In the remake ceasars mother passes her genetic mutation to ceasar, the mutation that makes her intelligent. I think the significance of this scene is relating to scully having alien DNA and passing it on to her son william. I also think that william may be possibly going by a different name since being adopted, just like Milo's name being changed to ceasar. I think its significance isnt just about william, but also about the mothers in this hospital because their babies are being genetically modified. There are so many references to planet of the apes in the x-files series. Here is a link detailing a few instances. http://x-files.wikia.com/wiki/Planet_of_the_Apes