Black Comedy: The death of the two Stokes brothers is portrayed as funny. One of them finally comes up with a good and clever wish — a new pair of legs at that moment. Precisely at that moment their home blows up, and the legs land next to Mulder and Scully who are coming to question them.
Blah Blah Blah: [Jenn reading a draft of Mulder's wish] "'Whereas, I have one wish left and desire to use it most effectively for the good of all mankind...' Yada, yada, yada. "'Here on this plane of existence...'" Hmm... Hmm-hmm. What, are you a lawyer?"
Deader Than Disco: In-universe. Jenn claims people want her to make them cool like the Fonz or whoever is the big name now. Mulder snarks that she has been out of circulation for a long time.
Eye Scream: Discussed by Mulder in order to defy it. The idea of eyes growing on stalks is squicky enough.
Mulder: I have to be [a lawyer] with you. (...) I'm not going to leave you any loopholes. I'm not going to let you interpret this as an edict to bring back the Third Reich or to make everyone's eyes grow on stalks.
Facepalm: Scully is embarrassed that she invited some scientists from Harvard to see a proof of paranormal which unfortunately disappeared. She facepalms with both her hands.
According to this episode, Benito Mussolini once used Jenn to gain power.
Mulder tries to write his last wish in legalese so that it cannot be misinterpreted and used as an excuse to bring back the Third Reich.
Too Dumb to Live: The Stokes brothers. One of them lost his legs in a car accident when they were smashing stuff with a baseball bat while driving in a car. They simply cannot come up with normal wishes and they are not Genre Savvy enough to word carefully their wish to reverse the mess their original wish caused. They really had it coming.
Wasteful Wishing: Anson Stokes' first wish was that his boss would shut the hell up. He did. Poor guy, his mouth got literally shut up.