The case file number (found in Mulder's briefcase in his Comity hotel room) is 3x99. This is the "episode" designation number for game in the X-Files series (like episode 3x24 is the episode "Talitha Cumi"). For all intents and purposes, the X-Files Game is a season 3 episode.
The "episode"'s title is "Agrippa", which appears in the game as the name of Wong's boat, as well as in the Bible found in Scully's Comity hotel room.
The graffiti on the warehouse wall by the boat dock ("Eat the Corn") is a reference to an off-color remark once overheard by Gillian Anderson. A grip in the Vancouver X-Files crew suggested that one of his colleagues "eat the corn" from a substance excreted regularly by most mammals. Anderson adopted the phrase and has been known to use it on occasion.
One of the flyers on the board in the FBI Conference Room advertises "Yoga -- instructed by David". This may be a reference to David Duchovny, who practices yoga and who had a yoga instructor on set while filming his scenes for the game in Seattle.
Craig Willmore (you - in the game) is a name we've heard before. In the episode "Syzygy", Margie & Terri give their Siskel & Ebert style rating to a basketball player named Craig Willmore (they give him a thumbs down).
Detective Astadourian (played by Paige Witte -- great last name) is named for Mary Astadourian, chief researcher and office manager at Ten Thirteen, as well as Chris Carter's personal assistant ("Astadourian" was previously used as the name of an observatory in the season 3 episode "D.P.O.").
James Wong is a shady character in the game, but the real James Wong was a staff writer (one of the greats -- partnered with Glen Morgan) during seasons 1, 2, and 4. See the in-jokes pages for those seasons for many, many references to James Wong and the episodes he has written.
Eventually you visit the town of Charno. Sarah Charno was a staff writer during season 2, and her husband Stu Charno portrayed the confused killer in the episode "Clyde Bruckman's Final Repose".
Gordon's Hauling may be named for writer Howard Gordon.
Your character, Craig Willmore, lives at Eavelyn Apartments. Halle Eavelyn was the Executive Producer of the game.
In the game the coroner's name (Joan Truitt) is very similar to the name of the coroner from the pilot episode (John Truitt).
Late in the game you receive an e-mail from a "Monte Joffin". Jon Joffin is the Director of Photography for the game and worked on the TV series.
References to Past Cases
On both your desk and your partner's desk is a mug with the slogan "Big Blue" from Heuvelman's Lake (a reference to the third season episode "Quagmire")
Agent Willmore is obviously taken with the Civil War (as you can tell by looking around his office). This fascination references Mulder's experiences in the episode "The Field Where I Died".
In the lobby of Mulder & Scully's hotel is an advertisement for Fairfield Zoo, complete with a picture of Sophie, the gorilla from "Fearful Symmetry"
Mulder & Scully were staying at the Comity Inn -- Comity is the name of the city in the 3rd season episode "Syzygy" (which was an in-joke in the episode itself -- see the Season 3 In-Jokes entry on "Syzygy" for more info).
One of the items you can collect from Mulder's room is the book "From Outer Space" by Jose Chung (a reference to season 3's "Jose Chung's From Outer Space" -- in case you couldn't figure that one out for yourself)
Also in Mulder's room you can find Vodka & Orange Juice (his drink of choice from "Syzygy"), a copy of "The Magic Bullet" (the paper published by the Lone Gunmen), and an advertisement for Sweet Potato Pie (his desert of choice from "Jose Chung's From Outer Space"). Try calling the number on the advertisement -- you will get a recording claiming that "You can't eat just one piece!".
Whenever you turn on a television (Mulder's room, Scully's room, your apartment) you get a continuous loop of Keystone Cops (a reference to "Syzygy").
We find that Agent Willmore is an aspiring author -- as evidenced by the rejection notice on the sofa in Willmore's living room. Willmore's rejection is much like that of the Cigarette Smoking Man's from the episode "Musings of a Cigarette Smoking Man".
Among James Wong's belongings are a dead frog and pieces of the game from season 3's "Hell Money". You can also find the "Hell Money" itself on his boat.
The paper bag listing the train yard rural route is from Clays BBQ -- which is the restaurant Mulder & Scully dine at in the episode "Red Museum".
Those "Special" Numbers:
517 - Your car's license number is 621517. This is the case number in the episode "Apocrypha", and the 517 represents the birthday of writer Frank Spotnitz's wife.
One of the files on your desk contains the address "1121 N. Menadra". 11/21 is the birthdate of Chris Carter's wife, Dori Pierson.
You must visit Rural Route 1121. 11/21 is the birthdate of Chris Carter's wife.
Using the ING on Agent Willmore's computer, you can see that Detective Astadourian's birthdate is 10/13/69. 10/13 is Chris Carter's birthdate (as well as Mulder's, and the name of the X-Files' production company).
The Easter Eggs:
Use the game's instructions to determine the names of some of the programmers and software developers (found in the list of credits). Use the ING on Agent Willmore's computer to do a search on their "Criminal" history. You will then see their picture and a brief description of their criminal records.
When Scully calls you from the airport, try shooting the woman in brown who walks in front of Scully. Shooting the woman triggers a small Easter Egg (the woman is one of the game's lead programmers).
In the world of computer programming, Easter Eggs are secret "tricks" or messages hidden by programmers during a software package's development. Often these Easter Eggs contain credits or the names of the people who worked on the programs. The X-Files game has a few Easter Eggs.