I've decided to go and make a definitive list of the game files/formats to help whoever wants to mod the game or create tools.
ROOM FILESSTxxx.DAT: Those are all of the rooms files, containing a compressed .TIM texture (4bpp and 8bpp images) + palette right after, Gian header + body (Sound format of the PlayStation version, deprecated in the PC version as all of the sound files are now .wav disguised as .DAT files in the SOUNDS folder), a little segment pertaining to footstep sound, other compressed TIMs + palettes (Which usually are characters like Rick, Gail, dinosaurs or puzzle textures) and lastly a compressed segment which contains room flags, triggers, 3D models and text strings (Which are at the very end of each room file and need a custom character table).
Something to note: ST60E (Which is an unused room) is the only room that actually has the last segment (Room data segment) uncompressed rather than compressed.
The PC version of the game has no differences regarding rooms files but it has several new rooms (STAxx.DAT, STBxx.DAT, STCxx.DAT) for the PC-exclusive WipeOut Internet mode. Also Arrange Mode (Again, exclusive to the PC version) has their own stage files.
Here's a complete list of room files:
https://drive.google.com/file/d/18J3vclPCgbn7bA3MrddMnQElRN5QUbibST1.DAT - ST9.DAT: Room data, flags, ecc.. of each stage floor (In order: 1F, 2F, S1, Facility Outdoors, S2, S3, Operation Wipeout Mission 1, Operation Wipeout Mission 2, Operation Wipeout Mission 3)
BIN FILESAAA.BIN, AREA_JMP.BIN, BK_EDIT.BIN, DBMODULE.BIN, EM_SET.BIN, EM_TEST.BIN, OAT_EDIT.BIN, PL_DEBUG.BIN, SAT_EDIT.BIN, SCR_LIT.BIN, SYS_DEB.BIN. VRAMVIEW.BIN and all of the TEST.BIN files (Except for TEST_MOT.BIN): Most likely leftover stuff from the developers that used to have debug functions within the builds. They are mostly 4 bytes long files.
CLEAR.BIN: A similar file to one of the segments of the CLEAR.DAT file with a few differences here and there, unused by the game.
LUKE.BIN, MOT.BIN, SEQ_EDIT.BIN, TEST_MOT.BIN: All these files are pretty similar, looks like a list of several .MD and SKN files. Nothing used by the game.
OPENING.BIN, STx.BIN, WEPx.BIN, TITLE.BIN: Duplicates of existing segments in several .DAT files, they are unused in the game.
OTHERC_CHANGE.DAT: Contains a compressed texture of the costume change objects, Gian files and lastly a .bmp with the background image of the Character Change menu.
CAPCOM.DAT: .bmp of the Capcom logo used when starting the game.
CLEAR.DAT: Segments of the ending (Computer) sequence containing an uncompressed texture with 4bpp and 8bpp images, palette, several Gian files and lastly data of the sequence with text scripts and so on..
OPENING.DAT: Same as CLEAR.DAT but it's the opening (Computer) sequence. Also, the .TIM texture is compressed this time and there's texture+palette+3D model of Kirk (Used in the DECEASED part).
CORE.DAT: Texture and 3D model of Regina (Which are unused in this file because the game actually uses the other CORExx.DAT files), texture of the fonts, Gian sound files and an uncompressed texture+palette of the inventory menu (4bpp images but Regina's avatar which is 8bpp).
CORE00.DAT: Compressed texture+palette of Regina's default costume. Third segment is the 3D model and the last 3 segments are something related to data.
CORE01.DAT: Compressed texture+palette of Regina's army costume. Third segment is the 3D model and the last 3 segments are something related to data.
CORE02.DAT: Compressed texture+palette of Regina's battle costume. Third segment is the 3D model and the last 3 segments are something related to data.
CORE03.DAT: Compressed texture+palette of Regina's ancient costume. Third segment is the 3D model and the last 3 segments are something related to data.
DEMO1.TRG, DEMO2.TRG, DEMO3.TRG, DEMO4.TRG: Demo files played when you are idle in the main menu (Contains inputs, flags, ecc..)
ENDING.DAT: No clue on this one. Three generic segments related to the endings?
PAL.DAT: A generic file that appears in every PlayStation PAL version of the game (Italian, French, UK, Spanish). Something related to the game code?
Hxx.DAT / Pxx.DAT: Weapons/weapon upgrades related stuff (The first segments are Gian files, the rest is compressed stuff like stats, data, also 3D model?)
ITEM.DAT/ITEM2.DAT: All of the item images (Each image is 8bpp) + palettes. ITEM2.DAT contains items from the Ancient Type costume.
LOAD.DAT: Background image (.bmp) of the load savegame menu.
LOAD2.DAT: Unused duplicate of the file described above.
M__xx.DAT / MExx.DAT / MFxx.DAT / MRxx.DAT / MSxx.DAT / MTxx.DAT: Ambient noises / soundtracks. All of those contain Gian segments (Those are unused in the PC versions as they use their own .wav files in the SOUNDS folder)
OMAKE1.DAT: Background image (.bmp format) of the screen when you obtain the Army and Battle costumes.
OMAKE2.DAT: Background image (.bmp format) of the screen when you obtain the Ancient Type costume.
OMAKE3.DAT: Background image (.bmp format) of the screen when you unlock the Operation Wipeout mode.
OMAKE4.DAT: Background image (.bmp format) of the screen when you complete the Operation Wipeout mode.
OMAKE5.DAT: Background image (.bmp format) of the screen when you unlock the special grenade gun.
OPTION.DAT: Background image (.bmp format) of the option menu.
OVER.DAT: Background image (.bmp format) of the screen when Regina dies.
P_END.DAT: Background image (.bmp format) of the screen when you finish the game. (Excellent. You got mad skills!!)
STUFF.DAT: Palette + Image of the various credits shown in the credits movie (Unused in the PC version as they are embedded in the video file instead).
TITLE.DAT: Compressed .TIM image of the strings from the main menu (New game, Load, Easy, Normal, ecc..) + its palette, Gian segments, compressed data and lastly the main menu background (In .bmp format).
WARNING.DAT: Image background (.bmp) of the warning screen.
WIPE.DAT: Compressed .TIM image of the strings from the alternate version of the main menu + its palette. The last segment is the background image in .bmp format.
WIPE_SUB.DAT: Image background (.bmp) of the screen when you select the Operation Wipeout mode.
WIPE1.DAT: Image background (.bmp) of the screen when you are about to play the first Wipeout Mode mission.
WIPE2.DAT: Image background (.bmp) of the screen when you are about to play the second Wipeout Mode mission.
WIPE3.DAT: Image background (.bmp) of the screen when you are about to play the third Wipeout Mode mission.
DOOR FILES (I do have a complete doors file list but it's all in Italian, if somebody really need it I can translate it in English and post it here.)
DOORxx.DAT: All of the door files containing Gian segments, uncompressed texture+palette (4bpp - 160x40 image) and lastly a compressed segment containing the 3D model of the door and other data. The only exception is DOOR403.DAT which contains only the sound files and the compressed data segment with no 3D model (The door is actually unused).
DOWN00.DAT / UP00.DAT: A door file like the ones described above but it's for the stairs animations.
WIRExx.DAT: A door file like the ones described above but it's for the piping check passageway animations.
IMD Files (Those are exclusive of the PC version of the game, all of them just are normal .TIM files).
Exit.IMD: Screen that shows up when you are about to quit the game.
Grenade.IMD: Updated version of OMAKE5.DAT.
kc_mes.IMD / kc_mes2.IMD: Japanese fonts/strings.
Level.IMD: Strings from the main menu (Where you choose the difficulty level).
mugen.IMD: Screen that shows up when the game asks you if you want to equip the special grenade gun.
Return.IMD: Screen that shows up when you are about to return to the main menu.
t_image.IMD: Main menu background image (PC version).
Title.IMD: Strings from the main menu (Where you choose the game mode).
wipe1.imd: Wipeout Online background pre-mission image.
Wipeout.IMD: Strings from the Operation Wipeout menu.
wipet.IMD: Alternate main background image (PC version).
yesno.IMD: Yes/No strings (Only present in the Japanese PC version of the game).
There's also the game executable that contains hardcoded stuff and text strings like room names, item descriptions, item names and menu strings. The PlayStation version has .XAS (.XA packages) files for all the speech lines (They are in .wav format in the PC version) and the movie files (Intro, eliport cutscene, endings cutscenes, credits movie and demo video) are PlayStation .SRT files.
And that's pretty much it, I've tried to inspect the model formats of the game but I have 0 experience in that so I couldn't do much unfortunately. If somebody more knowledgable than me wants to go ahead and figure out how the model formats work then I'd be very happy to help.
