Every password, door access code, bank account, and terminal login that I can find are listed here. Some you can discover by playing the game, some are hidden, and some have been discovered by methods I can't discuss on an open channel. If you find something I've missed drop me an email and I'll add it.

jcd - bionicman
scarter - antique
jmanderley - knight_killer
ghermann - zeitgeist
ajacobson - calvo
anavarre - scryspc
jreed - redshoes
jreyes - amigo
klloyd - target

Alex Jacobson's Locker: 2001

Soda Machine Code: 9183
NSF Castle Clinton Stair Hatch: 666
Castle Clinton Computer and Security terminals: nsf - righteous
Paul's Hidden Cache: 4321
Paul's Hidden Cache Terminal: pdenton - chameleon
Bank Accounts (use at subway station):

543654 - 5544
312446 - 1351

Another Bank Account (use at 'Ton or Bar)

947761 - 2867

Free Clinic Surgery Bay: 2153
Free Clinic Terminals:

jallred - apple
alice_priest - secretary

Lift to Roof Code: 3316
Smuggler's Mirror Closet: 432
MJ12 Door Code: 2167
MJ12 Terminal Code: mj12 - coupdetat
MJ12 Barracks Login: jsteward - js1357
MJ12 Weapon Locker: 007
NSF Warehouse Basement Doors (opens more than one but not all): 2577
NSF Warehouse Security & Generator Terminals: nsf- righteous
NSF Warehouse Login (only for the basement room): tfrase - valleyforge

Check Mission #1 for all UNATCO codes.

Phone Booth Code: 6653
Brooklyn Bridge Station Women's Restroom Code: 5482
Airfield Terminal Login: etodd - saintmary
Hanger Access Code: 5914
Suspension Crate Code: 9905

Check Mission #1 for all UNATCO codes.

NSF HQ Security Login: tjefferson - newrevolution
NSF HQ Dish Alignment Terminal: mcollins - revolution
NSF HQ Transmitter Terminal: napoleon - revolution
Subway Access Code (Paul should tell you this if you complete his objectives): 6282

Detention Block Door: 4089
Detention Cells: 4679
Armory Code: 2971
Medical Area: 0199
LabNet Account: dmoreau - raptor
Research Facility Exit (given when you complete all objectives): 1125
R esearch Facility Security Terminal (works on most terminals)l: mj12 - Intruder
Research Facility Secuirty Terminal (works on ALL terminals): psherman - raven
Plasma Cannon Containment Code: 5239
Alternate UNATCO Computer Login: demiurge - archon

See Mission #1 for all UNATCO codes.

Purge Valve Code: 99871
Elevator Access Code (if you want to return to the MJ12 helicopter area): 989
Hidden Surveilence Room by Police Station : 22
Police Vault Code (Maggie Chow will give this code when you speak with her): 87342
Jock's Apartment Terminal: flyboy - 5x5
Queen's Tower Elevator Code to Renovated Floor: 3444
Queen's Tower Security Terminal: queenstower - security
Queen's Tower Elevator Bypass Code: 1709
Maggie Chow's Security Terminal (works in other terminals): mchow - insurgent
Dragon's Tooth Sword Door (Nod to BlackMajic for the code): 718
Quick Shop Terminals: management - code324
Luminous Path Compound - 1997
Tong's Terminal: jcdenton - sanctuary
VersaLife Work Terminal: all_shifts - data_entry
VersaLife Lab Elevator: 6512
Augmentation Canister Suspension Code: 5878
MJ12 Research Security: mj12 - security
MJ12 Research Terminals: mchow - damocles
VersaLife Level2 Code: 55655
Nanotech Wing Emergency Doors: 768
UC Cascade Shutdown: 525

Free Clinic Terminals:

jallred - apple
alice_priest - secretary

Ship Yard Entrance Code: 0909
Ship Yard Security: usfema - security
East Warehouse Code: 2249
West Steel Fence Code (just like that 80's song by Tommy Tutone): 8675309
Ramp Code: 6655
Ship Security Terminal (works deep inside the ship, not on the upper deck part except for one non-security terminal): root - reindeerflotilla
Ops Door Code: 83353
Engineering Bridge (used deep inside the ship): 9753
Ships Armory Code: 71324
Ship Terminal Access (only works in the captain's quarters) : kzhao - captain
Captain's Quarters Door Code: 65678
Computer terminal in Stanton Dowd's family mausoleum: SDowd - Illuminati

Maintenance Lift Code: 4003
Radioactive Area: 0001
Security Terminal Building #14: rzelanzny - shadowjack
Bank Account in Metropolitain: 2221969 - dullbill
MJ12 Catacomb Security Terminal: hela - ragnarok
MJ12 Security Shack (street level): streetstation17 - werewolf
Paris Bank Accounts:

005133 - salem008
002639 - aramis01
004418 - morbus13
001506 - naga066

Dance Club Storeroom Code: 1966

Chateau Logins:

nicolette - chad
bduclare - nico_angel

Sidon's Vault (Gold storage): 1942
Fountain of Wisdom (Gunther Showdown): 0022
Templar Terminal Login: 34501 - 08711
Bank Account (In Metro): 576001 - wyrdred08
Everett Security Terminal: meverett - pynchon
Morpheus Access Code: 8001

Bot Activation Code: 5868
Security Terminal: command - zebra42
Tunnel Security Temrinal: tunnel01 - omega2a
Control Room Terminal: gsavage - tiffany

Krakian Hatch: 1223
Storage Closet: 12
URV Bay Terminal: tech - sharkman
Alternate Terminal Login: apinkerton - antennapedia
Drilling Tunnel Code: 5690
Substation URV Terminal: oceanguard - kraken
Substation Security / Terminal Login: mj12 - skywalker
Silo Doors: 8456
Missle Silo Launch Terminal: elder - armageddon

Area51 Blast Door Code (from sentry tower terminal): a51 - xx15yz
Sector 2 Security Grid: 8946
Alain's Bed Bunk: 0169
Sector 3 Security - area51 - bravo13
Explosives Locker: 4225
Reactor Core Access: 2001
Stairwell Blast Door (aka Aquinas Access): 1038
Gray Lab Security (reverse name/password if it doesn't work): lab12 - graytest
Blue Fusion Reators Disable Code: 7243
UC Control Access Doors: 1234 (this isn't mentioned in the game so use it if you're just plain out of options)
Security Terminal Access to Aquinas Router Room: page - uberalles
Aquinas Router Login: icarus - panopticon
Aquinas Substation (This worked on the Aquinas Router room pre-game patch): 6765
Coolant System Access (doesn't seem to work with game patch): 2242

(Thanks for additional passwords Smithy665)