Occurrences of 11/21:

Chris Carter's Wife's Birthday (Dori Pierson) 11/21/48

Pilot - time on Scully's clock: 11:21

Deep Throat - Colonel Budahas' birthday: 11/21/48

Fire - the case is X-File #11214893

Miracle Man - Autopsy time: 11:21

Erlenmeyer Flask - time on Scully's clock: 11:21

Little Green Men - 1121's on 'WOW Signal' See WOW Signal here - thanks to Dennis Wittig

The Host - Autopsy case #DP112148 (initials & full b'day)

Irresistible - time on Scully's clock: 11:21

Colony - time on Scully's motel room clock: 11:21

F. Emasculata - Package #DPP112148 (initials & full b'day)

Paper Clip - Samantha Mulder's birthday: 11/21/65

Syzygy - Time Mulder brings first girl to police station: 11:48 (birth month&year)

Piper Maru - Flight 1121 to Washington

Talitha Cumi - time when Mulder first visits his mother at the hospital: 11:21

Talitha Cumi - time when Scully is working at her computer: 11:21

Unrequited - time when Mulder & Scully see the upset woman at the war memorial: 11:48 (birth month&year)

Redux - time one of the calls was made (from above Mulder's apartment): 11:21

Travelers - date Mulder first meets Arthur Dales: 11/21/1990

One Son - the time everyone meets at the air force base - 11:21

Millennium - the time the policeman stops to help Mr. Johnson with his flat tire - 11:21

William - time of the first scene in the X-Files office, with Doggett doing push-ups - 11:21

The Truth - the time Knowle Rohrer pulls up to the USMC Base Brig to "retrieve" Agent Mulder - 11:21

The Movie - the time Mulder goes to the Dallas Field Office, where Scully joins him and analyses the fossils: 11:21

The Movie - a number on one of the domes in Antarctica: 1121

Ground Zero (X-Files novel by Kevin J. Anderson) - Time stamp on chapter three - 11:21 a.m.

Antibodies (X-Files novel by Kevin J. Anderson) - Time stamp on chapter eleven - 11:21 a.m.

Occurrences of 10/13:

Chris Carter's birthday 10/13/56

Chris Carter's production company

Pilot - autopsy time: 10:56 (month & year)

Deep Throat - case file #DF101364

Deep Throat - thug's license number: CC1356 (initials,day&year)

Genderbender - according to Detective Horton, the time the victim entered the room with a woman: 10:13

The Erlenmeyer Flask - door # 1056 (month&year)

Little Green Men - 1013 on 'WOW Signal' See WOW Signal here - thanks to Dennis Wittig

The Host - John Doe #101356 (full birth date)

End Game - top of Mulder's letter - To: Dana Scully,001013

Paper Clip - Fox Mulder's birthday 10/13/61

D.P.O. - 10th high score on video game had a time of 10:56

2Shy - time Mulder & Scully get Incanto's skin test results back: 10:13

731 - Combination to unlock train door #101331

Apocrypha - door # where alien is held (& Krycek): 1013

Musings of a Cigarette Smoking Man - Security Council Resolution # for the immediate extermination of EBE's: #1013

Max - Time on Skinner's watch, 10:56 (month & yr)

Redux II - time when Mulder & Samantha are talking in the diner: 10:13

Emily - one of the dates on the manifest (assumed to be the date Scully's ovum were harvested)

How the Ghosts Stole Christmas - radio station Mulder is listening to: 101.3

Terms of Endearment - The time that the baby's body was placed in the fire

One Son - In the teaser, the date and time the members meet at the air force base - 10/13/1973, 10:56 (10/13 month & day, 10/56 month & year)

One Son - Time Spender is looking for his mother - 10:13

Millennium - "The time is near" -- the time on the grandfather clock when Frank and Mr. Johnson are discussing Frank becoming the Fourth Horseman

Requiem - According to the police dispatcher, the code for a downed aircraft is a "code 10-13"

Within - the number of Gibson Praise's file is "1013-113"

The Movie - countdown-time Mulder recites to Scully on phone - 13:56 (day & year)

The Movie Soundtrack - The "hidden" track on The X-Files: The Album takes place 10 minutes and 13 seconds into the last track

The Movie on Video - The X-Files movie was released on 10/13/1998.

Ground Zero (X-Files novel by Kevin J. Anderson) - Time stamp on Chapter two - 10:13 a.m.

Antibodies (X-Files novel by Kevin J. Anderson) - Time stamp on chapter twenty-two - 10:13 a.m.

Occurrences of 9/25:

Occurrences of 5/17:

We finally have an answer!
According to Trust No One, the Official Third Season Guide to the X-Files, there is no significance to the numbers 111471 or the letters JTTO -- they just keep appearing to keep us confused and guessing! Well, as long as they go through the trouble to tease us, I'll go through the trouble to keep listing them!
-- by the way -- an excellent suggestion by Diana Klingle-Wilson -- that the significance of 11:14 is that it is 10:13 plus one (10+1 = 11, 13+1 = 14 -- 11/14)