At certain points throughout the game you will find Weapon Racks containing "unique" weapons. These weapons are indicated in the Secondary Weapon Display with a question mark icon and are indestructible, unlike other secondary weapons. There are five of these weapons in all. For all but the Giant Hand, you will need the Scorpion Sword. The Garden Flamingo and Teddy Bear MUST be completed before you find the Mask, and require you to backtrack along the path you would take when trying to complete the towers in which they are located. The Teddy Bear also requires you to break a wall during the Dahaka chase zone in that area. The Giant Hand and Glowing Sword, you get one chance only to find them.
To get the secret ending, simply collect all 9 life upgrades. Then go to the hourglass room as you would normally would, get the Water Sword from Kaileena, and beat a secret final boss.