* Squeeze (1.03) – the first appearance of Eugene Victor Tooms (Doug Hutchinson), a man who breaks into people’s homes so he can steal their livers.
* Ice (1.08) – blatantly, yet enjoyably, influenced by The Thing with a terrific cast including Felicity Huffman and Xander Berkeley.
* Eve (1.11) – a creepy early episode about twins.
* Humbug (2.20) – the first time the show goes into kooky territory: a funny and off-kilter story about former circus acts. Scully eats an insect.
* Clyde Bruckman’s Final Repose (3.04) – Peter Boyle won an Emmy for guesting as a man who can predict people’s deaths.
* War of the Coprophages (3.12) – a delightfully witty and playful episode where Mulder goes solo to investigate weird goings-on… then keeps phoning Scully to discuss the case.
* Jose Chung’s From Outer Space (3.20) – a story told in contradictory flashbacks.
* Bad Blood (5.12) – the same events shown twice, once from Mulder’s point of view, once from Scully’s. (Same kind of ground as Jose Chung, but even funnier.)
* Drive (6.02) – Bryan Cranston guests as a man who must keep moving west at all costs…
* Triangle (6.03) – the best one of them all: time travel, actors playing multiple roles, long takes, a jazz soundtrack, and Mulder and Scully’s first kiss.
There are loads of great ones, though. Some honourable mentions…
* The pilot episode.
* Fire (1.12) – Mark Sheppard off of everything plays a man who can set anything alight.
* Beyond the Sea (1.13) – Scully loses her dad.
* Blood (2.02) – digital displays start telling people to kill.
* Død Kalm (2.19) – Scully and Mulder start aging rapidly).
* Oubliette (3.08) – Jewel Staite from Firefly gets kidnapped.
* Home (4.02) – THE FUCKED-UP ONE ABOUT INBREDS.
* Paper Hearts (4.10) – Tom Noonan guests as a serial killer.
* Leonard Betts (4.12) – Romano from ER gets decapitated several times.
* Never Again (4.13) – a man’s tattoo starts talking to him with Jodie Foster’s voice.
* Small Potatoes (4.20) – several babies in the same town are born with tails. It’s possible Luke Skywalker is the father.
* Unusual Suspects (5.03) – an origin story for the Lone Gunmen sidekick characters.
* Travelers (5.15) – the first X File is revealed in a flashback story set in the 50s.
* Dreamland (6.04/6.05) – Michael McKean swaps bodies with Mulder.
* How the Ghosts Stole Christmas (6.06) – some ghosts steal Christmas.
* Monday (6.14) – The X Files does Groundhog Day.
* Arcadia (6.15) – Mulder and Scully pose as a married couple.
* Milagro (6.18) – John Hawkes guests as someone who writes about murders before they happen.
* Hungry (7.03) – a story from the monster’s point of view.
* X-Cops (7.12) – presented as a fly-on-the-wall documentary.
* Hollywood A.D. (7.19) – Mulder and Scully’s work is adapted into a movie.
* Jo Souhaite (7.21) – a genie grants someone three wishes.
* John Doe (9.07) – Robert Patrick’s Doggett forgets who he is.
* The first movie’s not bad too.