The following items can only be collected once you know you need a certain potion: Tonic - In the tavern, off the shelf; Cricket - Under the girl's bed; Mushroom - In the bushes by the door to the girl's house; Egg - In the reeds next to the porch of the woodcutter's house; Potion - Bring the ingredients back to the Alchemist.
I'm not going to write a linear walkthrough because most of this game is just wandering around talking to NPCs and reading diaries to find out what to do. Instead, here's a list of where to find items: Pumpkin - Porch of woodcutter's home; Knife - Box on floor of Alchemist; Hammer - Drawer in Girl's bedroom; Candle - Above fireplace in girl's home; Jack-o-lantern - Combine pumpkin and knife, then carved pumpkin and candle (cont.)