Table of Contents
1. Spell Routine Offsets
2. Command Routine Offsets
3. Specialty Routine Offsets
4. Event Routine Offsets
5. Bug Fixes
6. Custom Routine Offsets (& Replacements)
A. Commands
B. Spells
C. Event Instructions
D. Patches
7. MiscellaneousWell this has been a long time coming, even I'm now having trouble keeping track of all I've found thus far, hehe. So I thought a separate thread to keep everything in a clean manner would make it easier to find and maybe others would be able to track down this information in a more efficient fashion.
I will list the Routine Maps as they appear in the Tower of Babil Docs (thereby ROM) for quick and easy reference (for myself and for others) I will have several links to the Tower of Babil Docs as well, to reference the routines I haven't done because they were completed long ago.
To find any of these values in ROM decrease the amount by 1FE00 (for v1.1) - They are in their LoRom format for efficiency purposes.

1/31/14 Added a Combo Patch which puts all of my released patches into one easy patch.

7/12/15 Finally cleaning this topic a little to put all of my work back into the main part of this topic.
This post is now updated with quick links to all of the available Command Subroutines I've commented on.
Spell Routine Offsets -00
Damaging Spells- 03D388
01
Damage, Sap - 03D3C2
02
HP Healing - 03D41C
03
Single Digit HP - 03D453
04
Drain - 03D476
05
Psych - 03D498
06
Status - 03D515
07
Immobilizing Status - 03D5B6
08
Add Image - 03D623
09
Reflect - 03D62C
0A
Life - 03D65B
0B
Heal/Remove All Statuses Except.... - 03D6F8
0C
Shape Changing Status - 03D82A
0D
Protect - 03D84F
0E
Shell - 03D873
0F
Slow - 03D897
10
Dispel - 03D8B0
11
Stop - 03D8EE
12
Peep - 03D924
13
Exit - 03D97F
14
Damage Based on Caster's HP - 03D99D
15
MP Recovery - 03D9F9
16
Elixir - 03DA19
17
Damage, Poison - 03DA2B
18
Damage, Status - 03DA73
19
Damage, Immobilizing Status - 03DA8C
1A
Sylph - 03DAAE
1B
Odin - 03DB5F
1C
Count - 03BB5
1D
Damage Based on Target's Max HP - 03DBE5
1E
Add Calcify - 03DC2B
1F
Gaze - 03DC90
20
Blaster - 03DCB0
21
Slap - 03DCCB
22
Mind Blast - 03DCF0
23
Hug - 03DCFB
24
Explode - 03DD12
25
Reaction - 03DD2F
26
Recover 1/10 of Max HP - 03DD4E
27
Damage, Status(Unused?) - 03DD92
28
Spawn Monster - 03DD98
29
Black Hole - 03DDAE
2A
Attack Based on Physical Power - 03DDC6
2B
Recover 1/3 of Current HP - 03DD62
2C
"Trigger A Reaction" - 03DDD9
2D
Invincibility Counter-On - 03DDD6
2E
Invincibility Counter-Off - 03DDDA
2F
Revive Monster - 03DDDE
30
Tradeoff(Suicide, bring in Next Monster) - 03DE31
31
End Battle - 03DFCF
32
Search - 03DFD5
33
Hatch - 03DFE8
34
Rydia Returns - 03E004
Command Routine Offsets00
Fight - 03C499
01
Damage Routines - 03C924
02
White/Black/Call/Ninja/Spell Item Routines - 03CC46
03 Spell Subroutines (Above)
04
Peep/Study - 03E153
05
Enemy Runs Away - 03E1B2
06
Steal- 03E1CC
07
Salve/Medicine - 03E2DC
08
Throw/Dart - 03E34C
09
Change/Row - 03E3D1
0A
Regen - 03E3FA
0B
Twin - 03E46F
0C
Cover - 03E60F
0D
Off - 03E653
0E
Gird/Endure - 03E696
0F
Kick - 03E6B4
10
Focus/Boost - 03EF70
11
Aim - 03E836
12
Pray - 03E852
13
Hide - 03E876
14
Show - 03E8BB
15
Sing - 03E900
16
Jump - 03E954
17
Parry - 03E9DE
18
Dark Wave - 03E9E9
19
Recall - 03EA1A
1A
Bluff/Boast - 03EAC3
1B
Cry - 03EAE6
1C
Part of Steal Subroutine - 03EB29
1D
Item - 03EB9D
Specialty Routine OffsetsDamage Determination - 03C9AF
Grimoire Item - 03EC0D
Out of Battle White Magic - 01B753
Full Disassembly on the Poison Status - 039E45/03A8FD
Full Disassembly on All Status Timers Event Instruction Offsets00 Load Some Type of Graphic FC (Actually Nothing) - 000000
01 Repeat XX Times the Following YY Actions EB - 000000(blank because this is looked at in respect to the Movement Patterns)
02 Play Visual Effect FD - 00C17C
03 Show Message from Bank 02 (Event Call) EE - 00E339
04 Open Namingway Screen D9 - 00E344
05 Open Fat Chocobo Screen D4 - 00E351
06 Bring Up Shop XX ED - 00E35E
07 Fade Song XX in EA - 00E379
08 Toggle Music Fade D8 - 00E38B
09 Fight Battle with Enemy Set XX EC - 00E391
0A Toggle Running D7 - 00E54B
0B Play Song XX FA - 00E559
0C Play Sound Effect XX FB - 00E56F
0D Add XX Character to Party E7 - 00E578
0E Remove XX Character from Party E8 - 00E6AF
0F Toggle Screen Tint XX F9 - 00E731
10 Toggle Screen Fade DA - 00E7C4
11 Put in Spell List XX' SpellBook, Spell YY E2 - 00E7D8
12 Restore HP (10 * XX HP) DE - 00E7FF
13 Restore MP (10 * XX MP) DF - 00E85F
14 Add Item XX to Inventory E0 - 00E8BF
15 Remove Item XX from Inventory E1 - 00E8CB
16 Toggle Status Ailments XX DB - 00E90A
17 Remove All Status Ailments but XX E3 - 00E929
18 Add Status Ailments XX E4 - 00E948
19 Add 100 * XX GP to Party E5 - 00E967
1A Subtract 100 * XX GP to Party E6 - 00E97E
1B Change Character Graphic to XX DD - 00E9B6
1C Inn DC - 00E9E6
1D End Event FF - 00EA20
1E Pause XX Cycles E9 - 00EAB5
1F Show Message 1XX (Yes/No Box) F8 - 00EAE9
20 Bring up Item Selection Window F7 - 00EB0E
21 Screen moves up 1 tile and down 1 tile D6 - 00EB65
22 Toggle Screen Shake D0 - 00EB94
23 Screen Flash D1 - 00EB9D
24 Screen blur and unblur D2 - 00EBD4
25 Travel to/from Moon D3 - 00EBEF
26 Open a Door D5 - 00EC17
27 Load Map FE - 00EDB1
28 Show Message from Bank 02 (Map Call) EF - 00EF28
29 Show Message 0XX from Bank 01. F0 - 00EF4E
2A Show Message 1XX from Bank 01. F1 - 00EF5F
2B Show Message XX (from Bank 3) F6 - 00EF70
2C Set Event Flag XX F2 - 00EF81
2D Clear Event Flag XX F3 - 00EF8A
2E Activate NPC XX F4 - 00EF93
2F Deactivate NPC XX F5 - 00EF9C
Visual Effect OffsetsBug FixesEnemy Evasion FixEnemy Magic Evasion FixInfinite Arrow Fix99% Evasion through Immune Byte FixLingering x4 Weakness through Immune Byte FixCustom Routine Offsets (& Replacements)CommandsFight(Broken Calcify Weapon Routine) to Fight(Imbued Weapons)Peep to SeekPeep to GeomancyCry to FFIV:CC CryCry to Coat HammerSteal to MugSalve to Item MasterDart to Draw Out(Katana Soul)lTwin to W.Meteo/Third Random Spell TwinTwin to Targeting Dependent Spell Used TwinAim to SnipeAim to BarrageAim to ArrowstormPray to Hunt(Empty Space) to Hunt Rewards System(Empty Space) to Hunt Rewards System +Hide to Advnc (Advance)Dark Wave to Dark Wave - Zombie DeathDark Wave to FFIV:DS DarknessDark Wave to Dark Wave + Spell CastItem to Not 100% Item AccuracySing to Harp-Dependent Sing(Empty Space) to Magic WeaponsRecall to Dragon SpeakRegen to Will Based RegenKick to No Armor-Improved Kick.Gird to FFI Based Armor-GirdBoast to Elemental Weapon(Empty Space) to Seek RemasteredSpells Healing Spells to Alchemy-CureDamaging Spells to Item Lore-DamageWeak to LOCKShell to SLO1Modify Speed to TMPRHug to FASTReaction to SLO2Dispel to SABRChillyfeez's Dispel to AuraCount to HARMCounte to Elemental Strike/Fancy FlourishBlink to RUSEOdin to AFIR,AICE,ALIT,ARUB, WALL, FEARProtect to Spell Power Dependent ProtectBlast to Magic SwordDamage, Sap to Piercing SightSearch to TauntSylph to Battle SkillDamage, Status (Unused) to Regen (Command)SpecialtyAuto-Hide to XX Armor = Dark Wave replacing CoverRedundant Start of Game Code to Storing Commands in RAM!PatchesImbued WeaponsKatana SoulBattle SkillsGeomancyFF III Style SingFFV Style Magic WeaponsCombo Patch of the above 6 PatchesMiscellaneousAmount of Free Space contained within BanksAudiovisual Code BreakdownOutside of Battle Treasure AcquiringChance to Drop Money while running and Stat ReplacementAuto-Hide Notes 1Auto-Hide Notes 2All Attack Building FormulasAuto-Cover NotesFighting Zeromus without Cecil.Command Menu AccessesBack Attack/Ambush/First Strike CodeLevel Up Code and NotesShadow Slot ProcedureBig Chocobo Coding (some)Damage TilesDisabling Level+Shield Defense MultipliersEnabling all items to be checked and decremented in the Item Use EventEnabling Critical Hits for FoesStat Changing AI RoutinesBow/Arrow Index Routines 1Bow/Arrow Index Routines 2