WARNING! EXTREMELY LONG POST!
Here's what I know:
<c:\Games\FreeSpace2\data\cache> - Cached Files, for faster loading. File Type is .ibx. These are automatically created by FreeSpace Open if they don't exist, so you really don't need them.
<c:\Games\FreeSpace2\data\cbanims> - Command Briefing Animations. File Type is .ani (and possbly .eff, I'm not sure). Associated Retail VPs are tango1_fs2.vp, tango2_fs2.vp, and tango3_fs2.vp.
<c:\Games\FreeSpace2\data\effects> - Weapons effects, explosions, shield hit effects, nebulas, etc. File types are .ani, .neb, .pcx, .jpg, .tga, .dds, and .eff. Associated Retail VPs are sparky_fs2.vp and sparky_hi_fs2.vp.
<c:\Games\FreeSpace2\data\fonts> - Never used it, I assume it's for replacing the default fonts. File Type is .vf. Associated Retail VP is sparky_fs2.vp.
<c:\Games\FreeSpace2\data\force feedback> - Never used it. File Type is .frc. Associated Retail VP is sparky_fs2.vp.
<c:\Games\FreeSpace2\data\freddocs> - Fred Manual.
<c:\Games\FreeSpace2\data\hud> - Any thing you see on the HUD. Escort list, Shield display ani's, all the gauges, the talking pilot heads, etc. File Type is .ani (and possibly .eff, I'm not sure.). Associated Retail VPs are sparky_fs2.vp and sparky_hi_fs2.vp.
<c:\Games\FreeSpace2\data\intelanims> - Contains the animations you see when you select Intelligence in the Tech Room. File Type is .ani (and possbly .eff, I'm not sure). Associated Retail VP is smarty_fs2.vp.
<c:\Games\FreeSpace2\data\interface> - All the buttons, menu layouts, frames, etc. File Types are .ani and .pcx (and possibly .eff and the other image formats, I'm not sure.). Associated Retail VPs are sparky_fs2.vp and sparky_hi_fs2.vp. (Note: sparky_fs2.vp and sparky_hi_fs2.vp also put some very interesting concept art in here, including 2_crim29.pcx, which is a ship that I don't recognize, but think that someone should make, now that we have triggered animation code.)
<c:\Games\FreeSpace2\data\maps> - Contains the textures for the ships. File types are .ani, .pcx, .jpg, .tga, .dds, and .eff. Associated Retail VP is sparky_fs2.vp.
<c:\Games\FreeSpace2\data\missions> - .fc2 (Campaigns) and .fs2 (Missions) go here. Associated Retail VP is root_fs2.vp.
<c:\Games\FreeSpace2\data\models> - Contains the actual 3d representations of the ships. File Type is .pof. Associated Retail VP is sparky_fs2.vp.
<c:\Games\FreeSpace2\data\movies> - Contains the in-game cutscenes. File Types are .mve and .ogg.
<c:\Games\FreeSpace2\data\multidata> - An alternate place to store some of the data collected when you play multi. Can be used by setting an option on the Multi option menu, but shouldn't be used, as it doesn't seem to work, and will keep you from playing any missions in Multi that are transfered from another player.
<c:\Games\FreeSpace2\data\music> - Contains the music files. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is warble_fs2.vp.
<c:\Games\FreeSpace2\data\players> - Files related to players. This directory contains saved HUD setups (when you hit the save button on the HUD Config menu). File Type is .hcf. Associated Retail VP is root_fs2.vp.
<c:\Games\FreeSpace2\data\players\images> - Contains pilot images. File Type is .pcx (and maybe other image types, I'm not sure.) Associated Retail VP is root_fs2.vp.
<c:\Games\FreeSpace2\data\players\multi> - Contains your multi player pilots. File Type is .plr.
<c:\Games\FreeSpace2\data\players\single> - Contains your single player pilots. File Type is .plr.
<c:\Games\FreeSpace2\data\players\squads> - Contains squad images. File Type is .pcx (and maybe other image types, I'm not sure.) Associated Retail VP is root_fs2.vp.
<c:\Games\FreeSpace2\data\sounds> - Contains sound effects (as opposed to music.). Should never actually have files in it. Associated Retail VP is sparky_fs2.vp.
<c:\Games\FreeSpace2\data\sounds\16b11k> - I actually don't know the difference between these this folder and the next one. It appears to just be the quality of the sound, but I can't be sure. File Types are .wav (and possibly .ogg, but I'm not sure.). Associated Retail VP is sparky_fs2.vp. Sounds to listen to in this section of sparky_fs2.vp include copilot.wav.
<c:\Games\FreeSpace2\data\sounds\8b22k> - Sounds to listen to in this section of sparky_fs2.vp include bup.wav, Pirate.wav, and thankyou.wav.
<c:\Games\FreeSpace2\data\tables> - .tbl (Regular Tables) and .tbm (Modular Tables) files go here. Common examples are ships.tbl and weapons.tbl. Associated Retail VP is root_fs2.vp.
<c:\Games\FreeSpace2\data\voice> - Contains the voice recordings for the game. Should never actually contain any files. Associated Retail VP is stu_fs2.vp.
<c:\Games\FreeSpace2\data\voice\briefing> - Contains the voices you hear both before the mission and during it. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is stu_fs2.vp. Sounds to listen to in this section of stu_fs2.vp include Gshi_AC_01.wav and MT10_MB_01_OUTTAKE.wav.
<c:\Games\FreeSpace2\data\voice\command_briefings> - Contains the voices you hear during command briefings. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is stu_fs2.vp.
<c:\Games\FreeSpace2\data\voice\debriefing> - Contains the voices you hear during debriefing, including the rank promotion and medal acquisition voices. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is stu_fs2.vp.
<c:\Games\FreeSpace2\data\voice\personas> - Contains the automated messages you hear from the pilots and Command in-game. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is stu_fs2.vp. Sounds to listen to in this section of stu_fs2.vp include 1_stray.wav, 2_Oops1.wav, 3_p_dead.wav, 3_traitor.wav, 4_backup.wav, 4_notarget.wav, 4_traitor.wav, 5_oops1.wav, 5_traitor.wav, and 7_Traitor.wav.
<c:\Games\FreeSpace2\data\voice\special> - Contains miscellaneous voice files. File Type is .wav (and possibly .ogg, I'm not sure.). Associated Retail VP is stu_fs2.vp. Sounds to listen to in this section of stu_fs2.vp include BAS_W3_01.wav, BAS_W3_02.wav, BAS_W4_01.wav, BAS_W4_02.wav, L2-2_SN_02a.wav (Make sure your speakers are at max for this one, it's really quiet.), LP1-2_SN_02.wav, LP2-1_A2_02.wav, LP2-2_SN_02.wav (Make sure your speakers are at max for this one, it's really quiet.), LP2-2_SN_03.wav, LP2-2_SN_03_OUTTAKE.wav (Which is apparently the source of the copilot.wav mentioned earlier.), and LP2-2_SN_06_OUTTAKE.wav.