In Mystery Dungeon, items play a very important role to assist your advance. While existing items such as certain berries and evolutionary equipments are included, the majority of items are entirely new and are designed to serve specific roles in the dungeons. As described in the Main Menus section, the item menu is the first option outside the dungeons, and the second option while in the dungeons.
Items are generally scattered in the dungeons or are sold at the Kecleon Shops at the Pokémon Square. However, certain important items are stored in special rooms inside the dungeon which require special items or skills to access.
The most common is the locked chamber.
In both the Sun Cave and the Western Cave dungeons, there will be various keys scattered throughout the floors, and these are required to unlock these chambers. To use the keys, stand right front of the locked chamber door and face it, then use the item from the menu. The chamber should open up and you can enter to obtain the item.
Another common barrier that locks out the items is water. You must use a water Pokémon as the lead to waddle across the water to get the item.
Sometimes the item will be entirely surrounded by a wall. To get through it, either bring along a Pokémon that knows the skill rocksmash to break the wall, or use a ghost Pokémon (note that certain ones like Dusclops and Sableye can't) to walk through the wall. Equipping your Pokémon with the special Passthrough Scarf will also enable them to do so.
Note that these barriers can co-exist for certain locations. For instance, you will need the key and a water Pokémon to get the item. Sometimes the locked chamber has the apperance of a simple wall, in that case, you could go in either by the key or by breaking the wall.
Remember that in this game, you are able to ditch any kind of item, even important ones such as HMs. Fortunately, if you happen to lose one of these important items, they will reappear where you found them. Otherwise, you will find a Link Cable in place of these items in these places.
As you can only bring a maximum of 20 items on each dungeon mission, store the rest at the Kangaskhan Warehouse at the Pokémon Square.
In the later dungeons, occasionally you will come across some Kecleon's Stalls inside the dungeons. Certain items such as the King's Rock are reported to be found here only. You could get around without paying, but it will lead to a catastrophic change on that floor. When Kecleon asks for the payment and you refuse, it will start to attack and call upon a massive surge of Kecleons on the same floor. They are all quite powerful, and so if you're on a low level, better pay than get killed.

Accessories

These are items which effect will not take place unless you equip your Pokémon with it, except the evolutionary scarfs, which should be placed in your item bag and used while in the Light Cave during evolutions.

Picture: Name: Effect: Location:
Customer Scarf Pokémon will not receive damage from confused companions, but hunger will decrease when such incidence occurs  
Defense Scarf Increases defense  
Passthrough Scarf Enables Pokémon to walk through walls or walk on lava ground Received from Gengar after clearing the Dark Cave
Pecha Scarf Pokémon will not be poisoned  
Stealth Scarf Sleeping wild Pokémons will not wake up  
Substitute Scarf Tossed items cannot hit  
Trap-evade Scarf Pokémon will not be affected by traps  
Warp Scarf Pokémon randomly warps off  
Bounce Ribbon Items tossed out by this Pokémon return naturally  
Free Ribbon No Effect  
Friend Ribbon Increases chance of recruiting wild Pokémon when held by leader Far-off Mountain Top 30/F (requires key)
Golden Ribbon Sells High  
Hunger Ribbon Hunger drops Quicker  
Lucky Ribbon Gains experience when Pokémon receives damage  
Restore Ribbon Speeds up HP healing but also speeds up hunger index decrease  
Special Ribbon Increases sp.attack  
Stamina Ribbon Hunger drops slower  
Cloud-Nine Bandana Does not get affected by weather  
Curve Bandana Tossed items can take a curved path  
Power Bandana Increases attack  
Through Bandana Tossed items hit all foes along the same direction  
Zinc Bandana Increases sp. defense  
Detect Band Raises evasiveness  
Loud Band Wakes earlier from sleep  
Munchlax Band Raises attack and sp.attack, but hunger drops quicker  
Persim Band Prevents confusion  
Snipe Band Easier critical hit on foes  
Stern Band Hunger drops slower, doesn't work in walls  
Sticky Headband Prevents item disabling from traps  
Twist Band Attack and sp.attack cannot be lowered  
Alert Glasses Held items cannot be taken  
Discover Glasses Knows where hidden items and foes are  
Insomnia Scope Never sleeps  
Lock-On Glasses Tossed items hit foes easier  
New Glasses Tossed items cannot hit  
Rootless Scope Tossed items may change directions  
Scope Lens Easier Critical Hit  
See-through Glasses Able to know where the enemy and items are on the same floor  

Tossed Items

Items that can be used to hit foes with, especially Shedinja who is resistant to common tackles. Note that the enemies may use such items to hit you as well.

Picture: Name: Effect: Location:
Twig Deals direct damage  
Cacnea's Needle Deals direct damage  
Corsola's Spike Deals direct damage  
Golden Tooth Deals direct damage  
Graveler's Stone Also Hits Foes in Walls  
Iron Spike Deals direct damage  
Pebble Also Hits Foes in Walls  
Silver Needle Deals direct damage  

Food

These are items important to keep your hunger index high.

Picture: Name: Effect: Location:
Apple Restores 50% hunger, will increase max hunger value by 5% if eaten when full  
Banana Restores 50% hunger, will increase max hunger value by 5% if eaten when full  
Big Apple Restores 100% hunger, will increase max hunger value by 10% if eaten when full  
Chestnut Restores 10% of hunger, favoured by Mankeys  
Grimer Food Restores 30% of hunger, but always induces a status condition  
World's Best Food Increase max hunger value by 10% and completely restores hunger  

Berries

Works pretty much like in the previous games. All restores 5% of hunger

Picture: Name: Effect: Location:
Cheri Berry Heals paralysis  
Chesto Berry Heals sleep  
Oran Berry Restores HP by 100  
Pecha Berry Heals poison  
Rawst Berry Heals burn  
Sitrus Berry Restores full HP, increase max HP by 2 when HP is full  

Gummies

These are important to raise your Pokémon's smartness. Pokémon of different types like different gummies. When eaten a gummy it favours, the hunger index is also restored by 60%, all other will be 25%. If the gummy is eaten when it is in the Friend Area, one random stat will also increase by 1.

Picture: Name: Effect: Location:
Black Gummy Favoured by Dark types  
Blue Gummy Favoured by Water types  
Brown Gummy Favoured by Ground types  
Gold Gummy Favoured by Psychic types  
Green Gummy Favoured by Bug types  
Grey Gummy Favoured by Rock types  
Navy Gummy Favoured by Dragon types  
Orange Gummy Favoured by Fighting types  
Pink Gummy Favoured by Poison types  
Purple Gummy Favoured by Ghost types  
Red Gummy Favoured by Fire types  
Silver Gummy Favoured by Steel types  
Sky Blue Gummy Favoured by Flying types  
Sprout Gummy Favoured by Grass types  
Transparent Gummy Favoured by Ice types  
White Gummy Favoured by Normal types  
Yellow Gummy Favoured by Electric types  

Seeds

Can be eaten or thrown, restores hunger by 5% when eaten.

Picture: Name: Effect: Location:
Dopey Seed Inflicts doped condition  
Dynamic Seed Inflicts 20 set damage when thrown. Inflicts 45 set damage on self and foe if eaten  
Eyedrop Seed Able to see invisible Pokémon  
Free Seed No effect, remains of Resurrect Seed  
Heal Seed Heals all kinds of status  
Hunger Seed Hunger index drops by 10%  
Life Seed HP goes up by 3  
Lucky Seed Increases level by 1  
Quick Seed Raises pace of walking  
Resurrect Seed Unusable, but automatically resurrects team member when fainted  
Sleep Seed Inflicts Sleep  
Squint Seed Unables to see things temporarily  
Teeter Seed Inflicts confusion  
Temporary Seed Makes foe unable to move temporarily  
Unfortunate Seed Decreases level by 1  
Warp Seed Warps elsewhere on the same floor  

Stat Enhancers

Works pretty much like in the previous games. Hunger restores by 5% when taken.

Picture: Name: Effect: Location:
Booster Raises power of the shortkeyed attack  
Calcium Raises Sp.Attack  
Iron Raises Defense  
PP Max Raises nove's PP to their max  
Protein Raises Attack  
Zinc Raises Sp.Defense  

Special & Evolutionary Items

Picture: Name: Effect: Location:
Melody Stone Used for wishing at the Wish Cave Receive from Medicham after rescuing it / Wish Cave 50/F
Rock Parts Regirock's protection, needed for Orgel Underground Ruins 15F
Ice Parts Regice's protection, needed for Orgel Underground Ruins 25F
Steel Parts Registeel's protection, needed for Orgel Underground Ruins 35F
Orgel Makes Mew appear at Underground Ruins when held Rock, Ice and Steel parts automatically merge to form this
Key Needed to open key chambers Sun Cave, Western Cave
Connect Box Allows you to connect moves without having to visit Gulpin's Connect Shop  
PokéDollar Money  
Beautiful Scarf Needed to evolve Feebas Western Cave 59/F (requires key)
DeepSeaScale Needed for certain evolutions Big Sea 15/F
DeepSeaTooth Needed for certain evolutions Big Sea 25/F
Dragon Scale Needed for certain evolutions Flying Dragon Hole ~30/F
Fire Stone Needed for certain evolutions Fire Great Land 29/F
King's Rock Needed for certain evolutions Wish Cave Kecleon's Stall
Leaf Stone Needed for certain evolutions Wish Cave Kecleon's Stall
Link Cable Needed for certain evolutions In place of HMs in key chambers when the item is already possessed
Metal Coat Needed for certain evolutions Southern Hole ~50/F
Moon Ribbon Needed to evolve Eevee into Umbreon Northwind Great Land 20/F (requires key)
Moon Stone Needed for certain evolutions Sun Cave
Sun Ribbon Needed to evolve Eevee into Espeon Flying Dragon Hole 20/F (requires key)
Sun Stone Needed for certain evolutions Sun Cave
Thunder Stone Needed for certain evolutions Lightning Great Land 29/F
Upgrade Needed for certain evolutions Wish Cave Kecleon's Stall
Water Stone Needed for certain evolutions Northwind Great Land 29/F

TMs & HMs

All 50 R/S/E/FR/LG TMs and 8 HMs are available in this game, with some HMs being critical to progress in the game plot. There are four additional new TMs.

Picture: Name: Effect: Location:
Cut   Underground Ruins 80/F (requires key and water Pokémon)
Fly Required to access certain dungeons Flying Dragon Hole (requires key)
Surf Required to access certain dungeons Sun Cave 20/F (requires key)
Strength   Underground Ruins 60/F (requires ghost Pokémon or Pokémon with rocksmash)
Flash   Underground Ruins 70/F (requires key)
Rock Smash Breaks walls Underground Ruins 45/F (requires key)
Waterfall Required to access certain dungeons Sun Cave 15/F (requires key)
Dive Required to access certain dungeons Given to you by Whiscash at the Whiscash Pond. If lost, Sun Cave 10/F (requires key and water Pokémon)
Excavate Breaks down wall in front  
Horizontal Cut Inflicts damage on 3 directions Faraway Sea 50/F (requires key)
Vertical Cut Inflicts damage on all 4 directions  
Vacuum Cut Inflicts 30 fix damage on everyone in the same room Faraway Sea 72/F (requires key)

Balls

These are items which cause a variety of effects in the dungeons.

Picture: Name: Effect: Location:
Alternate Ball Changes foe in front to another Pokémon specie found on the same floor  
Big House Ball Clears out all walls & water paths in the same room  
Blast Ball Enemies along the same direction all sent back against the wall  
Bounce-Back Ball Inflicts recoil damage on foe for a few turns when hit by physical attacks  
Clean Ball Restores disabled items by the glue trap  
Constrict Ball All foes on the same floor cannot move  
Crash Ball Sends enemy in front crashing into another enemy  
Double-Team Ball Increases evasiveness  
Dry Ball All lava ground and water dries up on the same floor  
Escape Ball Teleports everyone out of the dungeon  
Flash Ball Unveils whole floor  
Fill-Up Ball Turns lava ground or water in front to normal ground  
Gather Ball Gathers all team members together  
Hail Ball Induces weather effect hail  
Hypnotic Ball Puts all enemies to sleep in the same room  
Identify Ball Learns what items are held by the wild Pokémon  
Item-Change Ball Changes the item of the foe in front  
Item-View Ball Unveils all items on the same floor  
Mountain-Climb Ball Able to hurt foes within the immediately surrounding 20 squares  
One-hit Ball Faints enemy in front in one hit  
Passthrough Ball Able to go through walls and lava ground  
Place-Change Ball Switches position with enemy in front  
Probe Ball Unveils location of all foes on the same floor  
Proportion Ball Inflicts great damage on foe in front if it is bigger than you  
Pull Ball Brings all items on the same floor to you  
Quick Ball Increases walking pace of all team members  
Rain Ball Induces weather effect rain  
Rock Ball Has a similar effect to the move Rock Tomb  
Sand Ball Induces weather effect sandstorm  
Scare Ball Unnerves the foe in front  
Silent Ball Disables all attacks by the mouth of the foe in front  
Slow Ball Slows down the movement of all foes  
Smoke Ball Will not receive damage from enemy for 1 turn  
Snatch Ball Able to snatch all stat-raising moves of foes  
Staircase Ball Unveils location of the current floor's staircase  
Steal Ball Snatches foe's item when scoring hit  
Stop Ball Makes foe in front unable to move  
Strive Ball Halves own HP, foe in front down to 1 HP  
Substitute Ball Changes foe in front into a substitute  
Sunny Ball Induces weather effect sunny  
Teeter Ball Confuses all foes in the same room  
Threaten Ball Enemy in front cannot move, and warps to floor's starcase  
Through Ball Makes self immune to tossed items  
Transparent Ball Won't be detected by enemy  
Trap-Break Ball Disables all traps in the same room  
Trap Ball Randomly sets trap for the enemy  
Trap-View Ball Unveils all traps in the same room  
Warp Ball Warps all enemies in the same room away  
Whirl Ball Sends foe in front crashing in wall, inflicting 5 fix damage