The two young boys sitting near Mulder and Scully on the bus are Oscar and Felix, Gillian Anderson's sons.
Among the headstones seen in Arlington cemetery, one belongs to "Piper B Maru", who is Gillian Anderson's daughter and was born on September 25, 1994 (the date of death on the tombstone), while another reads "Julie Ng", who is a behind-the-scenes producer for the show.
"Phreaking" is a slang term for hacking a phone in order to gain free access to a telecommunication system allowing the user to make unlimited free calls, it also makes them much harder to trace. The term originally referred to groups who had reverse engineered the system of tones used to route long-distance calls. By re-creating these tones, phreaks could make free phone calls around the world. In modern times with the advent of digital phones that no longer use analogue dial tones phreaks use computers to hack their cell phone's software allowing them to connect to any telecommunication company's cell tower in the world giving them free phone service.
The phrase at the end of the opening credits "accuse your enemies of that which you are guilty" is a phrase used by Joseph Goebbels, the head of the Nazi propaganda machine during World War II. During a speech he gave at one of the Nuremberg rallies he said "the cleverest trick used in propaganda against Germany during the war {first World War} was to accuse Germany of what our enemies themselves were doing." Many think this was an attempt by Adolf Hitler to justify the impending imprisonment and slaughter of Jews to the people of Germany by telling them that it's okay for them to do it because everyone else is secretly doing it anyways.