Some of my favourite X-Files episodes (in no particular order):

• Syzygy (written by Chris Carter; directed by Rob Bowman)
  Two teenagers in a small town share a birthday, and when the planets are in a special alignment on this birthday all hell breaks loose. Mulder and Scully are also affected (presumably) by this planetary alignment. ;)
• Memento Mori (written by Chris Carter, John Shiban, Frank Spotnitz and Vince Gilligan; directed by Kim Manners)
  Scully finds out that she has cancer - an inoperable brain tumor. While Mulder searches for answers and a possible cure; Scully, on the other hand, decides to seek treatment at a hospital where other abductees have received help for similar health problems.
• Pusher (written by Vince Gilligan; directed by Rob Bowman)
  Robert Model seems to be able to bend others to his will - quite often resulting in others' deaths. Mulder and Sculy investigate these mysterious cases, and get caught up in Modell's plans personally.
• The Post-Modern Prometheus (written by Chris Carter; directed by Chris Carter)
  Mulder and Scully investigate a case in a small town - where women are getting mysetiously impregnated. A bizare story, with a 'modern-day' Frankenstein.
• Chinga (written by Stephen King and Chris Carter; directed by Kim Manners)
  Scully goes on vacation, only to be caught up in a case where individuals in a small town in Maine are attacking themselves, and a child's toy seems to be the culprit.
• Small Potatoes (written by Vince Gilligan; directed by Cliff Bole)
  Mulder and Scully investigate when a number of babies in the same town are born with tails. The case soon focuses on a man who can seemingle change his appearance at will.
• Irresistible (written by Chris Carter; directed by David Nutter)
  Mulder and Scully investigate a case where a man murders women to collect their fingernails and hair. Scully is particularly disturbed by this case, but doesn't want to admit it to Mulder. Donnie Phaster is a very frightening and convincing villain, revealing that some of the most disturbing cases involve humans, instead of the paranormal.
• Clyde Bruckman's Final Repose (written by Darin Morgan; directed by David Nutter)
  In the course of tracking a serial killer preying upon fortune tellers, Mulder and Scully come upon a man whom Mulder considers to be a genuine psychic. Reluctant to cooperate with the investigation, the psychic already has visions of how the case will end -- with Mulder's death.
• War of the Coprophages (written by Darin Morgan; directed by Kim Manners)
  Mulder investigates a series of deaths that seem to be tied to cockroaches, while Scully assists - and debunks - by phone.
• Jose Chung's From Outer Space (written by Darin Morgan; directed by Rob Bowman)
  When a couple claims to have been abducted by aliens, Agents Mulder and Scully try to get at the truth but everyone has a different version of the story, including the "aliens" themselves.
• Bad Blood (written by Vince Gilligan; directed by Cliff Bole)
  Mulder and Scully have different versions of why and how Mulder staked a suspect (yes, like a vampire) through the heart - and they must get their stories straight before reporting to Skinner...
• Triangle (written by Chris Carter; directed by Chris Carter)
  Mulder goes in search of a ship that has disappeared in the Bermuda Triangle in 1939. But when he gets on board, Mulder finds that he--and all the passengers and crew--are still stuck in the past.
• How the Ghosts' Stole Christmas (written by Chris Carter; directed by Chris Carter)
  On the night before Christmas, Mulder convinces Scully to put aside her gift wrapping and stake out a reputed haunted house. But in the house, they discover a married couple keeping a dangerous secret.
• The Unnatural (written by David Duchovny; directed by David Duchovny)
  Mulder and Scully dig up an old case involving a star player in the Negro Baseball League with an unbelievable batting average -- and an incredible secret.
• Je Souhaite (written by Vince Gilligan; directed by Vince Gilligan)
  Blah
• all things (written by Gillian Anderson; directed by Gillian Anderson)
  Scully encounters an old lover and mentor in a chance incident at a hospital, and this meeting puts into place a number of events that make Scully question her current path in life.
• Requiem (written by Chris Carter; directed by Kim Manners)
  Billy Miles, the teenager from Mulder and Scully's first case together, asks for the agents' help. Mulder and Scully investigate a mysterious crash and disappearances, while Scully suffers from dizziness and fainting spells. Mulder investigates the woods alone on a tip that there is a UFO hidden there, and a hunch that Scully might be abducted if she joins him.
• Redux II (written by Chris Carter; directed by Kim Manners)
  With Scully lingering near death and the future of the X-Files in danger, the Cigarette Smoking Man comes forward with a surprising offer to save Scully's life--and more.
• Ice (written by Glen Morgan and James Wong; directed by David Nutter)
  One of Mulder and Scully's early cases takes them to the Arctic Circle, where a team has disappeared, only leaving a video of something that has gone horribly wrong.
• Beyond the Sea (written by Glen Morgan and James Wong; directed by David Nutter)
  On a night that Scully has a vision of her father, she learns that he has died of a heart attack. Mulder and Scully visit a convicted serial murderer (Luther Lee Boggs) who says that he has psychic powers and can rescue some teenagers that have been kidnapped. Mulder is the skeptic this time, but Scully is reluctant to disbelieve, especially when Boggs says he can let Scully speak to her father for one last time.
• One Breath (written by Glen Morgan and James Wong; directed by R.W. Goodwin)
  Mulder recieves a phone call that Scully has been found alive--barely alive. While Scully lies in a coma in an intensive care unit of a local hospital, Mulder tries desperately to give her a reason to live. Mulder also confronts the cigarette "Smoking Man" about his possible role in her abduction.
• Wetwired (written by Matt Beck; directed by Rob Bowman)
  Agents Mulder and Scully uncover a dark conspiracy behind a bizarre series of seemingly unrelated murders in a small town. As the extent of the conspiracy is revealed, Scully's trust in Mulder is put to the test.

Some episode summaries taken from the x-files episode guide, others written by myself. In general, crappy ones my me. :)