2007-07-05 (updated 2016-06-01)
Syntax:
locked object : code [lock location] [code found from]

Listed in order of encountering the locked object

Reception & Marine HQ
Combat Prep : 584 [Marine HQ] [Bill Tyson's PDA near the location on second visit to Marine HQ]
Locker #001 : 396 [Maintenance] [Kitchen, Adam's PDA] – automatically opened and emptied on return trip if not opened by player
Locker #023 : 531 [Energy Stab. Unit] [Baston's PDA right next to it]
??? Possible missing code for something here around this portion of the game?
Locker #017 : 347 [Infirmary] [Caseon's PDA found right next to it]

Alpha Labs (no backtracking)
Locker #013 : 586 [Alpha Labs Hallway] [Dorweiler's PDA found right next to it]
martianbuddy : 0508 [North Hallway] [Moses' PDA found right next to it]

Alpha Labs Sector 1
Locker #009 : 752 [?] [Berger's PDA in nearby room]

Alpha Labs Sector 2
Locker #038 : 409 [MFS Compressor] [Chin's PDA in Engineering Security Checkpoint]
Locker #039 : 102 [Coolant Control Junction] [Connors' PDA in MFS Compressor]

Alpha Labs Sector 3
Locker #047 : 123 [Hazardous Materials Lift] [Lamia's PDA in Hazardous Waste Disposal]
Locker #048 : 123 [Coolant Monitoring] [Lamia's PDA in Hazardous Waste Disposal]
Locker #049 : 123 [EFR Staging Room 1B] [Lamia's PDA in Hazardous Waste Disposal]

Alpha Labs Sector 4
door : ? [Reactor Junction 1] [???; Unlocked if you free the scientist in the previous room]
Locker #064 : 651 [?] [Nelson's PDA]

Enpro Plant
Locker #063 : 972 [Power Core Access] [Chasar's PDA right next to it]
Plasma Storage : 734 [Maintenance 3] [Hammer's PDA in same large room]

Central Communications Tower
Locker #054 : 246 [Security Office] [Wolfe's PDA in Comm Systems]

Waste Recycling 2
Locker #003 : 483 [Monorail Access] [Sadowayj's PDA in Central Maintenance, Waste Recycling 1, and Johnson's PDA in Main Environment Control]

Monorail
Locker #003 : Open [Recycling Boarding Plat.] [None needed]
Monorail Airlock : 826 [Site 2 Transfer Area] [Ross' PDA in Site 2 Transfer Area]
Locker #054 : 142 [Site 2 Transfer Area] [Hollies' PDA right next to it]

Locker #078 : 364 [Delta Checkpoint Storage] [Cullen's PDA in Monorail Security Checkpoint]
Locker #079 : 364 [Delta Checkpoint Storage] [Cullen's PDA in Monorail Security Checkpoint]

Delta Labs 1
Locker #210 : 298 [Storage Room 21-D] [Price's PDA in Delta Entryway]

Delta Labs 2
Locker #112 : 538 [Records Office] [Cinder's PDA in Delta Ops Administration]
Locker #113 : Open [Records Office] [None needed]
M. Abrams office : 931 [Delta Security Junction] [Abrams' PDA in Kaczynski's room in Alpha Labs 4]
Locker #116 : 972 [Delta Security] [Terminal right next to it]
Locker #114 : 715 [Operations Server Room] [Post-it note on the side of the locker]
Locker #115 : Open [Operations Server Room] [None needed]

Delta Labs 2b
Locker #103 : 259 [Maintenance Corridor] [Erikson's PDA right next to it]
Locker #216 : 624 [Specimen Research Lab] [Michael's dialog just before]
Locker #217 : 624 [Specimen Research Lab] [Michael's dialog just before]
Locker #213 : 371 [Stasis Transfer Control] [Stemmon's PDA in Maintenance Area 4]
Locker #666 : 372 [Analysis Control] [Post-it note next to the locker numpad]

Storage 07 : 725 [Central Processing] [McNeil's PDA in Technical Director's Office nearby]
Martian Buddy : 0508 [Secure Storage] [Moses' PDA found in Alpha Labs]
Level 3 Access : 463 [Central Processing] [McNeil's PDA in Technical Director's Office nearby]

Delta Labs 3
Locker #317 : 841 [Terminal Office Storage] [Cerano's PDA in Lower Terminal Office]
Locker #386 : 836 [T1 Access] [Lee's PDA in Chamber 1 Control]
Locker #387 : 836 [T1 Access] [Lee's PDA in Chamber 1 Control]

Delta Labs 4
Locker #104 : 579 [Delta4 Security] [Downing's PDA in Delta4 Junction 2, also a terminal nearby]

CPU Complex
Locker #452 : 571 [Entrance Checkpoint] [Jackson's PDA in Delta Main Lobby in Delta before entering CPU Complex]
Lab A : 626 [Main Entrance Hall] [Bates' PDA in Security Monitoring, also seen through a security monitor nearby]
Locker #669 : 468 [Lab A Upper Floors] [Haskell's PDA in Lab A ???]
Locker #009 : Open [Lab A Upper Floors] [None needed]

The code listing will be completed when I bother to, which likely won't be anytime soon.

2008-06-27
While it is very clever and space efficient (I'm impressed by this trick) to hide a secret code inside the close option text of the spoiler tag rather than in the text area of the spoiler tag itself, this unfortunately hides the code permanently from people using plain text or script disabled browsers. Research shows that 10% of all web users fall into this category and this number is rising.

2008-06-27
this unfortunately hides the code permanently from people using plain text or script disabled browsers.

Somehow I doubt those (plain text browser) people play Doom 3 :) For script disabled (I prefer the NoScript addon over globally disabling everything)... ehh... they can't probably even view the Doom 3 website either, so I don't think it matters in their case much.

edit: I'll replace those with full code listing later on (I haven't recorded all yet). This will probably take some time as playing the game through on nightmare is tedious and isn't really my focus now.

2008-06-28
people with plain text browser go to one of the _good_ doom 3 homepages, such as zerowing.idsoftware.com/linux/doom. Faster, quieter, and you can possible even get away with downloading DOOM 3 using the company's server, while you boss is watching.