Many are a bit formulaic, some even boring, but some episodes are true gems, offering much more than initially meets the eye. It follows that those who aren't acquainted with the series could benefit from a viewing guide, so here are my suggestions.
As you may already know, there is a serial story thread which runs through all five seasons. However, none of my picks are integral parts of that storyline, except the pilot. The serial episodes can be good, and they do build on each other, but they are more for devotees. (After viewing the pilot you can tell if you're a candidate.) In my opinion, the storyline wears thin after the first few seasons. It was fun for a while, but after too many wholly unsatisfactory resolutions, this viewer is convinced there's no there there. I just can't get excited about mysteries that I know aren't going to lead anywhere.
By the way, see the official site for a complete episode guide. In the list below, (yy x nn) means season yy, number nn. Yes, the X-Files Movie: Fight the Future is not covered below. This is because it is storyline-related, and I don't think it measures up to Jose Chung or Clyde Bruckman.
Jose Chung's "From Outer Space"(3x20)
By sheer luck, this was one of the first few X-Files episodes I ever saw. When
I saw this, I thought it was the most stimulating television programming I had
ever seen. This episode is dense and rapid-fire, densely packed with bits of
classic UFO lore, simultaneously layered with alternative sceptic/believer
interpretations, somehow weaving them into a colorful fabric of fact and
delusion. As events transpire, you keep guessing which of the two possible
explanations will snap into focus, until . . . yet another explanation
shows up. Unfortunately, if you're not that familiar with UFO lore you
may miss some of the little jokes and clever symbolism which make this such a
superlative artistic accomplishment. Regardless, you should find it
entertaining.
Clyde Bruckman's Final Repose (3x4)
A tale of three psychics: one is how we would expect a psychic to be -- and a
fake. The others are disturbingly accurate, but not what we would expect (or
want) a psychic to be. "How could I see the future if it didn't already
exist?" one says, revealing himself to be a diehard fatalist, which, after
all, is what a real psychic would have to be. I've always thought that
time-travel stories made for shallow science fiction, until I found some that
confronted the paradoxes head on with clever devices. This story toys with
its paradoxes, all the while sustaining the element of mystery.
Humbug (2x20)
One of the funniest episodes, full of characters and situations that are
bizarre even by X-Files standards, and downright sick and twisted at
times. Heh-heh. (The Jim Rose Circus fills
out the cast.)
Post-Modern Prometheus (5x6)
This has to win some kind of award for starting out so bizarre and pulling the
pieces toghether. And of course the tribute to Frankenstein and the chutzpah
to actually shoot it in black and white must win some more.
War of the Coprophages (3x12)
A town is invaded by cockroaches that kill with mysterious powers, but
sometimes things aren't as supernatural as they seem. Sometimes it's just
space aliens.
Blood (2x3)
What I like about this episode is -- okay, it's a gimmick. But it's fun.
Pilot
The pilot set the tone for the series perfectly: strange happenings, a quirky
investigator, and a conspiracy to cover up what's going on.