Feel free to argue regarding episode placement or ones I snubbed.
  1. Jose Chung's From Outer Space
    The pinnacle. A barn burning meta-criticism of the X-Files, a unique commentary of the nature of memory and storytelling, Charles Nelson Reilly being Charles Nelson Reilly, two ridiculous cameos, and the best comedic line of the entire series: “I didn't spend all those years playing Dungeons and Dragons and not learn a little something about courage."
  2. Clyde Bruckman's Final Repose
    A surprisingly touching and human episode. Sad but incredibly sweet, with some incredible moments. Peter Boyle is incredibly great, and Clyde’s delicate relationship with Scully is what elevates this above the pack.
  3. Paper Clip
    It’s hard to pick from the early mythology episodes, since they’re all pretty enjoyable, but the scene at the mining facility (a UFO and ALIENS???) really make this one stand out.
  4. Humbug
    Just a fun, well done standalone episode that probes at the concept of our perception of normal. Also Scully eats a cricket.
  5. Home
    Probably the most disturbing, and talked about, non-mythology episode. I feel like this is the closest X-Files got to modern horror.
  6. Bad Blood
    Rashomon X-Files style. Super enjoyable but not as heady as Jose Chung.
  7. Duane Barry
    Another great early mythology episode. It’s hard to watch these and not think how bad and needlessly convoluted the later seasons' mythology eps became. Sigh.
  8. X-Cops
    It seems gimmicky, but X-Files through the lens of a Cops episode is very entertaining and holds up remarkably well years later.
  9. Triangle
    Another gimmick premise (uninterrupted takes, split screens) but the story and execution actually make it work. Scully passing herself in the split screens is one of those iconic X-Files moments.
  10. The Post Modern Prometheus
    Most popularly known as the black and white episode, this is The X-Files take on Frankenstein. Beautifully shot, intentionally hammy, great use of “Cher”, although viewed from a 2015 lens there’s some questionable rape apology in it. It could be argued this episode is non-cannon as it has comic-book-book-ends.
  11. Honorable mentions: Beyond The Sea, Anasazi, Piper Maru, Pusher, Small Potatoes, Paper Hearts