The comic book Chuck appears to be reading in the final scene is titled "Ex Machina," Latin for "From/of the Machine." This could be a reference to Chuck and the Intersect in his head, or to the dramatic arts term "deus ex machina," (literally "the god from the machine"), defined in contemporary times as any plot device which summarily resolves the major conflicts in a story. The diagrams Chuck has hidden in the comic would certainly qualify.
"Ex Machina" is written by Brian K. Vaughan, who also wrote the "Y: The Last Man" comic book series. A "Y" poster is one of several that can be seen on Chuck's bedroom wall in this episode.