Tomorrow night, The X-Files will air its first new episode since 2002. This fact may give you the desire to revisit the original run of the landmark sci-fi show, but it has 202 episodes and you can't watch all of them before tomorrow. Therefore I've picked one episode from each of the first 7 seasons that I think is worth consideration. Season 8 and 9 are when Doggett replaced Mulder, and I have not watched them since I was 13, so I won't be weighing in on those episodes.
Season 1: Beyond The Sea
A real downer of an episode to begin a marathon with, but it is simply one of the best of the entire series, and it is easily the best episode of season 1. The usual skeptic-believer relationship of the show is reversed when Scully meets a death row inmate who claims he can communicate with her dead father.
Season 2: Duane Barry
Another intense episode. Mulder attempts to negotiate a hostage situation with a man who claims he was abducted by aliens. The episode ends with a cliffhanger, setting up an arc for Scully that runs throughout the series, but the second part, "Ascension", isn't needed to enjoy this episode and is nowhere as good.
Season 3: Jose Chung's From Outer Space
After the strong emotions of those last two episodes, you need to watch a comedy episode, and writer Darin Morgan is the whole reason this show ever had comedy episodes. While "Clive Bruckman's Final Repose" and "War Of The Copraphages" are highlights, "Jose Chung's" is one of the most outlandish, wild rides the show ever took us on.
Season 4: Musings Of A Cigarette Smoking Man
While "Home", the episode about the inbred family of murderers, is definitely the most famous episode of season 4, what are you really getting from it? Shocks? Scares? I personally would rather watch this one. "Musings" featured the show's primary antagonist recounting stories from his younger years, placing him at historic events in almost unbelievable ways. While showing a more human side to the typically menacing and untouchable Smoking Man is used largely for comedic effect in this episode, it also gives us a deeper understanding of the man's pain, making him one of the most interesting villains in TV history.
Season 5: Bad Blood
Another great playful episode, "Bad Blood" features Mulder and Scully giving their own accounts of the same investigation, one that might have involved vampires. Much like "Musings", "Bad Blood" uses jokes to veil the fact that it's actually a character study. We get a presentation of the ways Mulder and Scully view themselves and one another.
Season 6: The Unnatural
I would guess "The Unnatural" is probably the episode that gets studied the most in academia. Written and directed by David Duchovny, the episode featured very little Mulder and Scully, or any other recurring characters from the show. Instead, it focuses on the story of an alien in 1947 who disguised himself as a black man and played on a baseball team. The show's signature extra-terrestrials were used as a metaphor for being an outsider even in the places where you most fit in.
Season 7: Hollywood A.D.
Comedy episodes just work best for this list. Go ahead and watch all of those 2- and 3-part mytharch episodes if that's what you're after, but if you waited for the night before the premiere to start your marathon, I think you just want some quick fun. "Hollywood A.D." was the second episode written and directed by Duchovny, but one that is much different from "The Unnatural". This episode features Mulder and Scully being shadowed by Garry Shandling and Téa Leoni (playing themselves) in preparation for an upcoming movie. In addition to the show poking fun at itself, "Hollywood A.D." features some great interactions between Mulder, Scully and Skinner.