This is from a thread I started on the Official Site's Message Boards back in November 2000 - check out the postings that I compiled this list from - here. Thanks to Aqua for editing!

1. In small town, USA running his own sunflower seed company.
2. Tied to my bed
3. In my shower (it's a wonder he got past dorm security)
4. Working as an Elvis impersonator in Vegas
5. Graceland
6. Lost in the woods (Think about it, they never even checked there)
7. The nearest erotic video warehouse, lost in the "X" aisle
8. cross dressing in Twin Peaks
9. umm, strip club
10. Lost in the kinky underwear section of Wal-Mart
11. He found Diana and decided to start a family with her (like in Amor Fati)
12. In a disco joint with cage dancers
13. At the ice capades with the Lone Gunmen
14. Hitting on a chick that knows everything about bugs
15. Knocking at my front door...what?
16. Beating the s**t out of Ratboy(pay-per-view entertainment lol)
17. Partying with the aliens
18. Getting piss drunk
19. Playing a game of 1-on-1 w/ me
20. In Massachusetts living it up with Dr. Bambi
21. Retiring in Florida with Arthur Dales I
22. Writing his book, Fox Mulder's "From Outer Space"
23. Opening up his own batting cage in Star, Mississippi
24. Trying on new speedos (the red ones have mysteriously vanished lol)
25. He's on his computer obsessively posting messages on this message board
26. Watching Monday Night Football with Krycek
27. Perhaps he's been hiding under his bed the whole time
waiting for the right time to jump out and yell, "Surprise!"
28. In Antarctica hoping that the aliens will return there for FTF: Part II, "Return to me"!!!
29. Area 51, of course.
30. In the bar having a little "drinkie"!
31. Up on Scully's apt. roof, finishing the antenna job that her landlord couldn't!
32. He's walking along the beach with his children, thanking the gods that he made 15,000,000. on that show that he doesn't really want to work on any more...
33. He's taking karate lessons so he can learn to actually fight so he can kick someone's (anyone's) a@@!
34. Still inside any shippers mind who is still holding onto the dumb hope that he will return and marry Scully (uh yes, and what's wrong with that!!!)
35. In a UFO!!!
36. Getting $50, 000 a year for endorsements
37. Disguised himself as Chris Carter and running a strange paranormal cult serious known as the x files
38. It was never Mulder, actually Eddie Van Blundht, who is now serving life in prison for knocking too many women up (plausible)
39. Hiding out from all his obsessive fans rocking and whispering quietly to himself. "This is not happening, this is not happening..."
40. In Scully (baby is Mulder clone)
41. In North Carolina visiting his mother's grave
42. Hooked up to that chair in my bedroom... (Tongue hanging out) rlrlrlrrllrl (that sound Homer Simpson makes when he thinks of food).
43. Making sure Fowly, Spender and CSM are really dead.
44. Making plans to take martial arts lessons to make sure that he can give Ratboy the ass whopping he is sorely in need of.
45. The aliens brought him back to the wrong woods and he's walking back.... from Germany.
46. If you really wanna know, follow the trail of lost cellular phones.
47. Spending an early retirement at a huge isolated sunflower seed farm.
48. He's really back in Oregon trying to scrub that orange x off the road that he spray painted there 7 years ago, because he feels guilty for having defaced public property.
49. He's left the Matrix!
50. Said 'Screw it' and uploaded himself along with Invisigoth.
51. Went to England to screw with Phoebe's head for a change.
52. Got lost at the Pentagon and is currently looking for his tour group.
53. Relieving himself in a dark alley.
54. Eating Chinese takeout with the LGM, while discussing their favorite adult film stars.
55. Having his cheeks severely stretched in the Arizona desert. *Ok, that's the obvious one*
56. Watching the Spice Girls Channel. (All spice, all the time)
57. Reading the New York Times, backwards.
58. Getting dragged around a neighborhood by a giant St. Bernard.
59. Went to the "Adult Film Awards'. Do you really expect him to come back anytime soon?
60. Went to a dentist appointment gone terribly wrong.
61. Currently a vampire trolling the L.A. Club scene for hapless victims.
62. Went in search of Scully's original hair color. 'The Truth IS out there.'
63. Lying in a large pool of money laughing his ass off.
64. Got locked out of his apartment and is trying to figure a way to get back in.
65. Suffering from severe cell phone withdrawal (not a pretty sight)
66. Canada (He realized that George W. Bush was about to be made president)
67. Going to a Cher concert with the great Mutato ;)
68. Mulder moved to LA changed his name to Sidney and is now dancing with the other girls at the local RUMBA ROOM making 4.75 an hour,
69. He is an anchor person for channel 16 news=WXFYL -they fired him when he tried to host LIVE with REGIS AND KATHY LEE
70. Stuck with Pee Wee Herman in a porn movie theater.
71. Mulder was upset when Scully went to Vegas without him and he's made his own trip.
72. Trying to figure out just how they get the caramel in Caramilk Chocolate Bars.
73. Trying to ban "Who Let the Dogs Out" from all radio stations.
74. Seeing how many licks it takes to get to the center of a Tootsie Pop. (Mulder: One thousand three hundred forty two.... one thousand tree hundred forty three....)
75. Invisible because he found another genie and is now stalking Scully. M: Scuuuullllyyy (ghostly voice) S: **bursts into sobs while some annoying woman sings in the background (lol, sorry the new music IMO is really lame)** Its almost as if I can here him and he were right here. M: **snickers** This is great. Now for my second wish... every porn video ever made.
76. Starring in a low budget porno
77. 2 words: Speedo Warehouse
78. Looking for the person who put that god-awful makeup on him in Amor Fati so he can kick their ass.
79. Stalking Richard Gere
80. Tracking down Britney Spears to see if she'll star in the next major porn video coming out.
81. Figuring out Blue's Clues
82. Searching for Scully's dog Queequeg
83. Trying to figure out how Christina Aguilera gets those jeans on
84. Tied up in the back seat of my car
85. Acting school, trying to learn how to show facial expressions and realistically cry
86. Stalking Scully and Doggett because he's jealous that Scully got a real man for a partner this time (Megan's Note: No, I don't agree with this one!)
87. Between my legs as I type this message
88. With his lover 4eva, Skinner
89. Lost.
90. At Gillian Andersons´ place doing...well we'll leave that up to your imagination
91. Singing the shaft theme song on a vibrating bed
92. Scrambling Scully's eggs - hey we never really did see what happened to them after Emily