Ok, I'll do them in sections, since that's how it's primarily done in the ROM, and it will make it easier to manage... these are explicitly changes to the weapons+armors.. w/o changing that much...
Rod, Hit Rate 50%
IceRod, Hit Rate 50%
FlameRod, Hit Rate 55%, Effective against Undead
Thunder Rod, Hit Rate 60%, Effective against Machines
Change Rod, Hit Rate 66%, Inflicts Mini status
Charm Rod, Hit Rate 66%, Casts "Bio", Inflicts Charm, Effective against Giants... I don't understand why a white magic spell is available for a Black Mage/Wizard's Rod...
Stardust Rod, Hit Rate 72%, Casts "Flare", Spell Multiplier = 3
Lilith Rod, 40 Attack Power, 70% Hit Rate, Effective against Giants, Flan, "Undead"
Staff, Hit Rate 50%, Casts "Peep", Effective Against Undead, Spirits
Cure Staff, Hit Rate 55%, Effective Against Spirits
Silver Staff, Hit Rate 60%, Casts "Esuna"
Power Staff, Casts "Berserk"
Lunar Staff, Hit Rate 66%, Casts "Blink"
Life Staff, Hit Rate 72%, Casts "Holy", Spell Multiplier = 3 or 4
Silence Staff, Hit Rate, 66%, Casts "Cure3", Spell Multiplier = 8
Darkness Sword, Inflicts Blind
Ancient Sword, 45 Attack Power
Medusa Sword, Inflicts Stone, Effective against Reptiles
Whip, Ice Elemental, Inflicts Paralyze, Effective against Reptiles
Chain Whip, Effective against Mages
Blitz Whip, Effective against Machines
Flame Whip, Effective against Undead, Casts "Fire3", Spell Multiplier = 4
Dwarf Axe, 70 Attack Power, Wind Elemental, +5 Str, Vit, Will, -5 Agi, Wis
Ogre Axe, 69% Hit Rate
Silver Knife, Effective against Undead (not Spirits)
Silver Sword, Effective against Undead (not Spirits),
Shuriken, Equippable by Edge, Consumable
Ninja Shuriken, Equippable by Edge, 60 Attack Power, Consumable
Poison Axe, 105 Attack Power, 60% Hit Rate, Effective against Dragons
Rune Axe, Inflicts Silence, 120 Attack Power, Casts "Cure4", Spell Multiplier = 8
Silver Hammer, Effective against Undead
Wooden Hammer, Casts "Lit-2", Spell Multiplier = 4
ShortBow, 50% Hit Rate
CrossBow, 55% Hit Rate
GreatBow, 60% Hit Rate
Archer Bow, 65% Hit Rate
ElvenBow, 80% Hit Rate
Samurai Bow, 70% Hit Rate, Effective against Giants
Artemis Bow, 75% Hit Rate, Effective against Dragons
Fire Arrow, 20 Attack Power
Ice Arrow, 20 Attack Power
Lit Arrow, 20 Attack Power
Darkness Arrow, 25 Attack Power, Inflicts Blind, Curse
Poison Arrow, Effective against Reptiles
Mute Arrow, Effective against Machines (not Mages)
Samurai Arrow, Effective against Flan
Medusa Arrow, Effective against Reptiles
Iron Shield, Resistant against Flan
Paladin Shield, Resistant against Spirits
Silver Shield, Resistant against Undead
Fire Shield, Resistant against Flan
Diamond Shield, Resistant against Machines
Samurai Shield, Resistant against Giants, considered adding a +3 bonus to something (probably Agi)
Paladin Helmet, Resistant against Spirits
Silver Helmet, Resistant against Undead
Samurai Helmet, Resistant against Giants, +3 Wis
Ninja Hat, Immune to Sleep, Paralysis
Glass Mask, 20 (or higher?) Magic Defense
Paladin Armor, Resistant against Spirits
Silver Armor, Resistant against Undead
Samurai Armor, Resistant against Giants, +3 Str, Vit
Crystal Armor, change Berserk resistance to Charm resistance
Power Robe, 20% Evade, 7 Magic Defense, 7% Magic Evade, +10 Str, Agi, Vit, Wis Considered making it equippable only by the girls
Paladin Gauntlet, Resistant against Spirits
Silver Gauntlet, Resistant against Undead
Samurai Gauntlet, Resistant against Giants, +3 Wis, Will
Dragoon Gauntlet, Edge can equip this
RubyRing, Immune to Piggy, Mini, Toad
Diamond Ring, Resistant to Machines
Protect Ring, Resistant to Holy, Darkness
Cursed Ring, +10 Str, Vit, -10 Agi, Wis, Will, Resistant vs all races

Should be nearly complete...