12 Discounted Jellies:
In the Ikushu resort town, due east of the entrance is a souvenir shop. There, they seem to sell only five items: a Pennant, a Jelly, a Key Chain, a Wooden Sword, and a Bear Figurine. However, between the first two items (Pennant and Jelly) is a line, which has been left blank for some inconceivable reason. If you scroll to it and try to buy the "blank" item there, you will not have a blank item added to your inventory, but rather you will end up having purchased 12 Jelly items for 5,000 Rupees - the significance of this being that 12 Jellies, at 500 Rupees each (as they are listed in that shop), cost 6,000 Rupees, saving you 1,000 Rupees.
Cursed Beads Abuse:
In the Lower Town of Hoverpool, in the building just to the north of the south entrance, is a man who will sell you the "Cursed Beads" item for 28,000 Rupees. The Cursed Beads item's main function is to transform into another item when used in battle, most often eight Seahorse Tongues. Seahorse Tongues normally cost 3,800 Rupees each, or 30,400 Rupees for eight. Thus, it is more cost-effective (by 2,400 Rupees) to buy some Cursed Beads and use them in battle rather than to buy Seahorse Tongues themselves.
The Falun Shield and it's Hidden Function:
Early in the game, as you visit Hoverpool for the first time, you will have to go through some sewers to dispatch a band of thieves. Connected to the sewers is the Hoverpool Wind Palace (the northeast corner of the sewers). If you sneak by everyone in the palace without speaking with them as you head to the southwest corner of the ground floor, you can enter a room and find the Falun Shield in a chest. This item normally would seem inferior to the Snapper Shield you could have already forged by now, and thus you'd be tempted to sell it. Doing so, however, is a very bad idea: using the Falun Shield as if it were an item (such as you would the Box Lunches) will refill your HP by 100. Thus, for a long time, the Falun Shield will surpass the healing abilities of most healing items you can get, although it's a fact not referenced in the game.