Version History:

0.9: Most of guide finished. Must finish Big Dungeon Changes after acquiring more MB and DLC dungeons after grinding.
0.98: I believe I am finished, though I wish to do some tidying up and double-checking.
0.98 and a half: Immediate mistakes fixed immediately.

This guide is simple, honestly. Use CTRL-F and type in what you're looking for. Everything is labelled as followed:

Monster Name: Monster Drop (Type of Drop)

Drop Types
Material - The most common drop type. Used for crafting plans.
Chip - Used in Disc Dev to create disks.
Medal - Can be turned in at Planeptune to obtain disks.
Plan - Certain Big Dungeon Changes drop powerful weapon plans
Item: Exam Location enemies drop items.

(Dungeon Change) and (Big Dungeon Change) may be before a monster if it requires that specific change to the dungeon.

Lastly, enemies such as Neptune?, Noire?, and Plutia? do not drop items in their initial forms, and only drop them if you let them transform (therefore, you cannot benefit from Destroy Symbols)

Virtua Forest Safe Zone
Dogoo: Dogoo Jelly (Material)
Tulip: Yellow Petal (Material)
Coin Man: Coin Fragment (Material)
Lizardman: Lizard Scale (Material)
(Dungeon Change) Magic Dogoo: Magical Jelly (Material)
(Dungeon Change) Forest Spirit: Mysterious Petal (Material)
(Dungeon Change) Dragon Knight: Knighted Scale (Material)
(Dungeon Change) Saint Whale: Small Whale Ball (Material)

Station Area
Bit: Small Conductor (Material)
Dogoo: Dogoo Jelly (Material)
Deus Man: Youth Heart (Material)
M-3: Crude Circuit (Material)
(Dungeon Change) Bug: Illegal Tech (Material)
(Dungeon Change) Black Spider: Strong Thread (Material)
(Dungeon Change) Rampaging M-3: Illegal SSD (Material)
(Dungeon Change) Magatsu Hinokami: Large Medal H (Medal)

Otori Forest
Contracted Angel: Mysterious Halo (Material)
Exhausted Jelly: Fancy Jelly (Material)
Sergeant Froggy: Teppachi (Material)
Hikky: Negative Sap (Material)
(Dungeon Change) Canopus: DL Only (Chip)

Zeca Ruins No.1
Pixelvader: Dot Antenna (Material)
Clyde: Rag (Material)
Ms. Clyde: Blue Ribbon (Material)
Cutekitty: Kupocat Claw (Material)
Contracted Angel: Mysterious Halo (Material)
(Dungeon Change) Canopus: DL Only (Chip)

Zeca Ruins No.2
Normal Shamparu: Shamparu Ear (Material)
Magical Shamparu: Shamparu Ear (Material)
Buff Shamparu: Shamparu Ear (Material)
Metal Dogoo: Metal Jelly (Material)
Dangerous Shamparu: Random Encounters (Chip)
(Dungeon Change) Scary Buff Shamparu: Slot (Chip)
(Big Dungeon Change) Crazy Buff Shamparu: Large Medal A (Medal)

Jet Set Range
Cardbird: Bird's Bronze Crown (Material)
Sunflowery: Sunflowery Seed (Material)
Pal Shell: Buff Stone (Material)
Alruane: Mysterious Petal (Material)
Fungus: Fungus's Spores (Material)
Shoebill: Large Beak (Material)
Ancient Dragon: Old Dragon...Orb (Material)
(Dungeon Change) Huge Dogoo: Premium Jelly (Material)

Wanderer's Cave
Frog-in-the-box: Cardboard (Material)
Healing Dogoo: Gel Feeler (Material)
Crystal Golem: Crystal Skull (Material)
Ice Skeleton: Ice Bone (Material)
Ice Boy: Frozen Cloth (Material)
Ice Girl: Pink Ribbon (Material)
Delinquint Cat: Gang Mask (Material)
Dolphin: Dolphin Tail (Material)
(Dungeon Change) Whale: Whale Ball (Material)
(Big Dungeon Change) Hero Craft: AG System (Material), Large Medal A (Medal)

Bandicrash
Terits: Purple Block (Material)
Spider: Spider Web (Material)
Plum-met: Plum-met Piece (Material)
Tokimeki Sister: Tokimeki (Material)
Phoenix: Phoenix Wing (Material), Histy (Accessory)
(Dungeon Change) Obese Dogoo: Prime Cut Dogoo (Material)
(Big Dungeon Change) Galactic Riser: Visual Memory 8x (Material), Large Medal B (Medal)

Kuzarat Facility
Poxvader: Round Antenna (Material)
Custom Bit: Illegal Conductor (Material)
Healing Dogoo: Red Gel Feeler (Material)
R-4: Illegal Memory (Material)
Matango: Matango's Spores (Material)
Created Soldier: Iron Fragment (Material)
R4i-SDHC: Magic Stone (Material)
(Dungeon Change) Killachine: Magic Dampener (Material)
(Big Dungeon Change) Alkaid: Dancing Controller (Material), Large Medal C (Medal)

Rud Arms Sewer North/South
Cold Boy: Frozen Cloth (Material)
Cold Girl: Pink Ribbon (Material)
Magic Stone: Magical Stone (Material)
Ice Golem: Ice Crystal (Material)
Lightbulb Angel: Mysterious Red Ball (Material)
Elemental Dragon: Dragon Claws (Material)
(Dungeon Change) God of Woe: Large Medal C (Medal)
(Big Dungeon Change) Replicant: Tough Replay (Material), Large Medal D (Medal)

Soni Wetlands:
Matango: Matango's Spores (Material)
Healing Dogoo: Red Gel Feeler (Material)
Lean Tuna: Cat Whisker (Material)
Heavy Dragoon: Magical Fragment (Material)
Nidhogg: Old Dragon...Horn (Material)
(Dungeon Change) Child Whale: Holy Whale Ball (Material)
(Big Dungeon Change) Achilles: Large Medal B (Medal)

Lowee Castle Interior/Exterior
High Bit: Illegal Gadget (Material)
Lowee Defense Guard: Iron Fragment (Material)
Child Wolf: Wolf Fur (Material)
Skeleton: Bone Fragment (Material)
Strange Person: Wicked Heart (Material)
Fenrir: Magical Wolf Fang (Material), Sleepy Cap (Accessory)
(Dungeon Change) Special Dogoo: Polygon (Chip)
(Big Dungeon Change) Rival Craft: Alloy Plate (Material), Large Medal E (Medal)

Underground Cave/Castle Chambers
Nanovader: Cell Antenna (Material)
Earth Golem: Earth Crystal (Material)
Aluna: Mysterious Petal (Material)
Strange Person: Wicked Heart (Material)
Lowee Soldier: Iron Fragment (Material)
Apeldoom: Red Petal (Material)
Lowee High Guard: Iron Fragment (Material)
Self-Defense System: Unexploded Shell (Material)
(Dungeon Change) Ice Whale: Monster (Chip)
(Big Dungeon Change) Doomsday Messenger: Guitar Controller (Material), Large Medal F (Medal)

Reload Grasslands
Boomerang: Bloody Boomerang (Material)
Apeldoom: Red Petal (Material)
WD Head: WD Fragment (Material)
Forest Turtle: Wood Shell (Material)
(Dungeon Change) Boss Lizard: Male-oriented (Chip)
(Big Dungeon Change) Pollux: Large Medal G (Medal)

Gigo Main Entrance
Kupokitty: Kupokitty Claws (Material)
Radisher: Radisehr Leaf (Material)
Swallowtail: Big Butterfly Wing (Material)
Horsebird: Horsebird Feather (Material)
Malvader: Nice Antenna (Material)
SDHC: Illegal Rom (Material)
King Crab: Large Pincer (Material)
(Dungeon Change) Killachine Mk-2: New Magic Dampener (Material)
(Big Dungeon Change) Zelgallion: Visual Memory 16x (Material), Large Medal G (Medal)

Halo Forest
Moulin Rouge: Red Seed (Material)
Rukh: Very Large Beak (Material)
Tarantula: Venomous Spider Web (Material)
Wolf: Wolf Pelt (Material)
Phoenix: Phoenix Wing (Material), Histy (Accessory)
(Dungeon Change) Nurse Binder: Newbie Nurse Cap (Material)
(Big Dungeon Change) Grafchocolo: Action Play (Material), Large Medal H (Medal)

Kobaba Ruins
Leanbox Soldier: Iron Fragment (Material)
Crack Tail: Yellow Petal (Material)
Missile Golem: Mithril Ore (Material)
Strange Person: Wicked Heart (Material)
Forest Crab: Crab Shell (Material)
(Dungeon Change) Sealed Calamity: Dragon Soul (Material)
(Big Dungeon Change) Epsilon: Large Medal I (Medal)

National Factory
High Bit Custom: Illegal Device (Material)
Inky: Venomous Cloth (Material)
Ms. Inky: Venom Ribbon (Material)
DSTT: Illegal Hardware (Material)
Heavy Tank: Unexploded Shell (Material), Face Visor (Accessory)
(Dungeon Change) Antares: Pronged Magic Damp. (Material)
(Big Dungeon Change) Opportune: Rare Plate (Material), Large Medal I (Medal)

Mines
Frozen Skull: Ice Skeleton (Material)
Ruffian Cat: Hoodlum Mask (Material)
Gold Lizard: Frozen Scale (Material)
Old Man Deus: Old Man's Pathos (Material)
Ice Fenrir: Freezing Claws (Material), Ehehe/Bleh Fox (Accessory)
(Dungeon Change) Unplanned Dogoo: Fancy Jelly (Material)
(Big Dungeon Change) Nemesis: Large Medal G (Medal)

Luji Plateau
Coyote: Sharp Fang (Material)
Wood Skeleton: Strong Wood (Material)
Death Stalker: Jet-Black Scale (Material)
Hachibei: Magical Contract (Material)
1000-Year Turtle: Ancient Shell (Material)
(Dungeon Change) Deneb: 1-Player Online (Chip)
(Big Dungeon Change) Fomalhaut: Large Medal N (Medal)

Zega Forest
Prince Cardbird: Bird's Silver Crown (Material)
Heretical Dogoo: Heretical Jelly (Material)
Alune: Mysterious Petal (Material)
Turtle: Turtle Shell (Material)
(Dungeon Change) Forest Whale: Journey (Chip)
(Big Dungeon Change) Big Pirachu: Large Medal J (Medal)

Haneda Mountain Range
Carroteer: Caroteer Leaf (Material)
High Heal Dogoo: Black Gel Feeler (Material)
Horsebird CAW: Horsebird Thigh (Material)
Wild Dog: Sharp Fang (Material)
Meow: Meow Claws (Material)
Dragon Warrior: Knighted Scale (Material)
Fenrir Wolf: Earth Ripper (Material)
(Dungeon Change) God of Catastrophe: Large Medal O (Medal)
(Big Dungeon Change) Trick Clown: Large Medal L (Medal)

Anonydeath's Lab
Blue Sun: Blue Seed (Material)
Ganglord Panther: Ganglord Mask (Material)
EDGE: Illegal RAM (Material)
Next-gen Bit: Illegal Tech (Material)
Bundodo Old Man: Hobby Soul (Material)
Panzer: Big Boom Shell (Material)
(Dungeon Change) Deus Ex Machina: 6-fold Magic Damp. (Material)
(Dungeon Change) Nihil: Evil Eye (Material)
(Big Dungeon Change) Ricky RELEASE: Large Medal R
(Big Dungeon Change) Gehachu: Large Medal T

Magma Cave
Magma Boy: Heat Cloth (Material)
Magma Girl: Black Ribbon (Material)
King Cardbird: Bird's Kingly Crown (Material)
Magma Crab: Molten Stone (Material)
Rafflesia: Poisonous Petal (Material)
Flame Skeleton: Flamin' Bone (Material)
Bincho:
Dolichorhynchops: Dolphin Check Tail (Material)
(Dungeon Change) Nihil: Evil Eye (Material)
(Big Dungeon Change) Gehachu: Large Medal T

Extradimensional Space
Spotted Plum-met: S. Plum-met Piece (Material)
Terist: Green Block (Material)
Speckle: TIny Outfit (Material)
Tera Hunk: Indulgence (Material)
Cerberus: Hell's Mane (Material)
(Dungeon Change) Cyber Whale: Death is the End (Chip)
(Big Dungeon Change) Viral Mareshimono: Large Medal V (Medal)

City Center
Numbing Spider: Paralysis Web (Material)
R-4 Custom: Illegal SSD (Material)
Promise Ring: Insane Contract (Material)
High Lizard: Blacklight Scale (Material)
Crescent Dragon: Old Dragon...Huh? (Material)
(Dungeon Change) Hakkei Hinokami: Large Medal X (Medal)
(Big Dungeon Change) Delphinus: Kinda-pissed Doll (Plan), Large Medal K (Medal)

Virtua Forest
Invader: UFO Controller (Material)
Jellyfish Dogoo: Gel Feeler (Material)
Forest Guardian: Earth Crystal (Material)
Sentientree: Negative Root (Material)
Forest Lord: Old Dragon...Head (Material)
(Dungeon Change) Forest God: Strategy RPG (Chip)
(Big Dungeon Change) Legacy: Large Medal Y (Medal)

EM ES Magma Cave
Mountain Seoi: Magical Stone (Material)
Blazing Skeleton: Molten Bone (Material)
Flame Flower: Burning Petal (Material)
Leanbox High Guard: Iron Fragment (Material)
Lost Dragon: Ancient...Thing (Material)
(Dungeon Change) Cat Knight: MO (Chip)
(Big Dungeon Change) Vert?/Green Heart?: Gungnir (Plan)

Lowee Castle Northen/Southern Space
Support Bit: Illegal SSD (Material)
Lowee Elite Guard: Iron Fragment (Material)
Magical Dogoo: Magical Jelly (Material)
Lowee Magical Soldier: Silver Fragment (Material)
Auto Surveillance: Illegal Rom (Material)
Lost Boy: Lost Holy Cloth (Material)
Lost Girl: Lost Ribbon (Material)
Ruin Guardian: Magical Core (Material)
Hyakushiki Weapon: Energy Pack (Material)
Ruins Dragon: Old Dragon...Ball (Material)
(Dungeon Change) Blue Whale: Baseball (Chip)
(Big Dungeon Change) Blanc?/White Heart?: CPU Crusher (Plan)

Duo R Ruins
Boxer Cat: Cat Gloves (Material)
Skull: Golden Tooth (Material)
Modded DSTT: Illegal Motherboard (Material)
Something Tree: Shaking Leaf (Material)
Vanargandr: Behemoth Claws (Material)
(Dungeon Change) Lost Soldier: MMO (Chip)
(Big Dungeon Change) Rom?/White Sister Rom?: Melee Pencil -G- (Plan)
(Big Dungeon Change) Ram?/White Sister Ram?: Metal Dogoo Pencil (Plan)

Do Temple
Dinosauroid: Super Hard Scale (Material)
Shimamo's Brother: Connecting Hook (Material)
M-3D: Crude Circuit (Material)
Promise Keeper: Contracted Ball (Material)
Suzaku: Flamin' Wing (Material)
(Dungeon Change) Ultradimension Dogoo: Yuriyuri (Chip)
(Big Dungeon Change) Uni?/Black Sister?: Linear Railgun (Plan)

Koagura Plateau
Orange Flower: Orange Petal (Material)
Flower Fairy: Mysterious Petal (Material)
Gray Wolf: Soft Wolf Fur (Material)
Gyps: Phantom Bird Wing (Material)
Cerberus: Large Fang (Material), Crab Ribbon (Accessory)
(Dungeon Change) Procyon: Many Resets (Chip)
(Big Dungeon Change) Peashy?/Yellow Heart?: Leopard Gloves (Plan)

Planeptune Alley
Death Boy: Death Cloth (Material)
Death Girl: Yellow Ribbon (Material)
Dragonia: Knighted Scale (Material)
ASIC Remnants: Iron Fragment (Material)
Dominance Machine: Magic Shell (Material)
(Dungeon Change) Killachine Prototype: Worldwide (Chip)
(Big Dungeon Change) Plutia?/Iris Heart?: Large Medal Z (Medal)

Digital Future Land
Shamparu Loner: Shamparu Ear (Material)
Dokidoki Sister: Tokimeki (Material)
NP-02v: That Blueprint (Material)
Bug Butterfly: Electric Wing (Material)
Wolf Blaze: Flame Wolf Emblem (Material)
(Dungeon Change) Super Galactic Dogoo: Galactic Dust (Material)
(Big Dungeon Change) VIRUS: Otton (Material)

Exam Location (DLC Location)
Jackal: Soft Wolf Fur (Material), Healing Rain (Item)
Mini Sister: Erde Crystal (Material), P. SP Charger (Item)
Platinum Dogoo: Amazing Jelly (Material), Nep Bull EX (Item)
Supportiove Typhon: Magic Shell (Material), STR Booster Z (Item)
Kaiser Phoenix: DLC (Chip)
(Dungeon Change) Sky Whale: Seamless (Chip)

Samusaran Highlands (DLC Location)
Social Bit: Illegal Tech (Material)
Regu: Electric Wing (Material)
Silver Dogoo: Magical Jelly (Material)
Gamobi Golem: Magic Stone (Material)
Arrows: 1-Player Online (Chip)
(Dungeon Change) Sashinkishu: Baseball (Chip)

Treasure Ruins (DLC Location)
Wild Horsebird: Horsebird Thigh (Material)
Spirit Echo: Death Cloth (Material)
Drago Battler: Super Hard Scale (Material)
Mithril Dogoo: Amazing Jelly (Material)
Spread Nighting: Female-oriented (Chip)
(Dungeon Change) Hakkakumagatsu Hinokami: Pretty Girl Game (Chip)