If I had to choose a one and only episode from the series, as I remembered it right now, it would be this one. I guess you'll get on my track, at least if you're looking at the show as a mystery show as it was intended to be to begin with, and not a love story or a sci-fi show for that matter.
Don't get me wrong, but I prefer the latter two rather as additional "spice", rather than the maintrack. For instance the chemistry is great between M&S here also no matter how you look at it. Also, I like the fact that it's almost like the viewer is through the eyes of M&S at the same time; the common sense of Scully but also the curiosity and the desire of Mulder.
At this point the possibilities was endless, and it was a great foundation to plan out the mythology story. There weren't as much effects and sci-fi blockbusters in the early episodes, but I believe that was actually X-Files strength and why the series worked best the less it tried to answer itself. The episode raised questions and it was in time what people knew and actually still know.
I can't spot any plot holes or anything either, everything seems to be in place. And while there were just as good similar episodes episodes in seasons 2-3, there's just something about the early season 1 which brings it above the rest in my opinion; the overall charm & mood plus the music.
Perhaps I'm biased with nostalgia, but I really think at least the music in the early season 1 was awesome and this episode is a great example. Not that I don't think Mark Snow was able to write even better stuff, but I believe he was commanded to tone his work down somehow later on.