Got into this game hardcore after 20 years. Been playing night and day lately & while this one wasn't made by Id, it appears to have a cult following and is critical to the series by diehard fans.
I had this originally on my N64 but can't find it or the console amongst all my gaming crap... er, stuff so I'm using Project 64 which I successfully setup a few days ago here.
Below is my progress thus far with many edits to follow, as well as many spoilers so turn away now if you don't wanna know 🙂

MAP01: Staging Area password: JC62 FD1P 9QCK FDJP

Secret level 1/4: MAP32 Hectic password: VBT8 9BD? 6?VK 9VK?

MAP02: The Terraformer password: BDF6 PQ28 1V6G B7TG or K7BQ ODYT MBQV D1JL

MAP03: Main Engineering password: 9TC3 5DYN C?NB NOVB

MAP04: Holding Area password: 857Z FQ1G LFMS HBVB
The 'blocks' code at the end of Level 4: Holding Area is 3,1,2,4 8)

Secret Level 2/4: MAP29: Outpost Omega password:  RNN7 8M?Y MWB0 B9KC

Level 5: Tech Center password: CP57 KNXY LK1F 6SKC
MAP05: Tech Center

Level 6: Alpha Quadrant password: B4Q2 KS0? 9GLD F9KC
MAP06: Alpha Quadrant

Level 7: Research Lab password: BMJ1 KSOP 7GDD P9KC
Red key location

Last of the U.A.C. levels!
MAP 08:Final Outpost: password: F33Z K1Y1 3GQ? X9SC

MAP09: Even Simpler password: PQ5M GDYX DCJN 59SB

MAP10: The Bleeding password: D7ZL GDZS BD3N FJSB (BFG 9000 on this level!)

MAP11: Terror Core password: NRSC H5X5 XCDQ N9QB

MAP12: Altar Of Pain password: M8BB H9XJ VCGQ X9QB

Secret Level 3/4: MAP30: The Lair: password: V87L 9C?8 C1JK 79VB

MAP13: Dark Citadel password: 4Q5K 48CX 854Q K9LB

MAP14: Eye of the Storm password: 375J K44W 9HBF 89VB

MAP15: Dark Entries password: 3TSM H9X5 BFNQ N9LB

MAP16: Blood Keep password: 28BK 68MJ 89Z6 WJLB

MAP17: Watch Your Step password: 2RHM 3JWF C4JO 6HVB

MAP18: Spawned Fear password: 19GH 5HPR 47CH BJVB

Secret level 4/4: MAP31: In The Void password: VR9M 9H?4 C1QJ Z9VB

MAP19: The Spiral password: 1RJM LKCM C4BO KJVB

MAP20: Breakdown password: O?LC ZGZO VFC2 FSVB

MAP21: Pitfalls password: ORR4 1KBX BH8G 2RVB

MAP22: Burnt Offerings password: Z8QM NKL8 C8HK WSVB

Map 23: Unholy Temple password: ZSSH ZGX4 3BK2 5SVB

MAP24: No Escape password: Y8VM LKBH C412 ?JVB

MAP28: The Absolution password: W83K O72O 7DC2 D9VB or W884 DGVN CRSH FFVB

These are only available through the Features cheat menu or password. Level 25 password kindly borrowed from Wiki.
MAP25: Cat And Mouse password: QY88 9BF6 6?DM 2BK?

MAP26: Hardcore password: TFY7 7BP2 46Q4 RBKT

MAP27: Playground password: PBHO YRYT 6T4G 5ZJP