A Penance egg is used to colour an Abyssal whip or a Dark bow in the rewards of Barbarian Assault. This is proven from the examine text of a coloured whip: A weapon from the abyss painted (colour here) from the yolk of a penance egg, although they never go into the player's inventory.
There are four eggs in which each cost 50 points, coming in the colours: White, Green, Blue, Yellow. Please note that if you use any coloured egg with an Abyssal whip or Dark bow, it will become untradeable. You may remove the colour from the weapon by using a Cleaning cloth. When you choose the egg colour, you must select which weapon you want to customize, and it will automatically be the colour you chose. Once you unlock an egg colour, you never have to pay the fifty points again to re-colour your Abyssal whip or Dark bow again.
It can take less than an hour to unlock all four eggs if you are able to find a good team that works together well.
Penance eggs are also available to be picked up in the game. When you are playing the game, the collector will be able to pick up three coloured eggs depending on what the call of the attacker is. The colour of the eggs are: Red, Blue, and Green. Red eggs are explosive eggs which deal heavy area of effect damage up to 3000s on the main target. Blue eggs have various debilitating effects depending on the type of creature. Green eggs give various buffs to targeted teammates. There are also yellow eggs, which the Penance Queen lays on wave ten; the only wave that you encounter the queen. These eggs undergo a readying process to be turned into an Omega egg to fire at the Penance Queen. Firing Omega eggs at the Penance Queen is the only way to defeat her.