There are always special items you find and they are stored in your Inventory (press Select and scroll using L and R) when found. They serve special purposes in making your way through the adventure.
The Inventory has 9 placeholders for nine items. I shall list the items in each row (starting from the top as the first row) from left to right.
Nicolas Flamel Book : Looks like an old book with a shining red dot in the middle. An item which assists in the finding of the Sorcerer's Stone.
Dittany : A sprig of fungi, one of Snape's Wiggenweld Potion ingredients.
Moly : A white flower with black stem. Another of Snape's Wiggenweld Potion ingredients.
Hagrid's Flute : Used to charm the Flobberworms to you. Play it using L button.
Bottle of Flobberworm Mucus : A small glass bottle containing the greenish Flobberworm Mucus.
Wiggentree Bark : A small piece of brown bark taken from Snape's stores. Another of Snape's Wiggenweld Potion ingredients.
Black Fire Potion : Made up of four ingredients. Used to get through the black fire in the dungeons to confront Quirrell.
Silver Tray : Used to store Pumpkin Pasties you find along your journey. Finding three means that you get an extra Energy Bolt added to your maximum Energy Bolt supply.
Wiggenweld Potion vial : Used to hold Wiggenweld Potion after you bring the ingredients to Snape during Potions class. If a vial is available, it helps to restore your Energy Bolts if you run out of them. However, one use drains the vial, but you can go back to the dungeons for a refill.