Halo 3 skulls
From Halopedia, the Halo wiki
Summary
A Skull in Halo 3 is an easter egg left in by Bungie to make the game more challenging or interesting, or to unlock potentials that would otherwise remain hidden. There is no information text to wield a skull, as there is with a weapon, but it can be picked up just the same, and its effects range from the useless to the terrifying. In Halo 2, these skulls were hidden very far out of the normal path of the level, sometimes even backwards. There is no reason to suppose that Halo 3 will change this.
In addition, the skulls now have some sort of importance to the Halo 3 Meta-game. They appear to multiply the amount of points you receive in the meta-game, meaning that picking them up will render you more than one benefit.
List of Known Skulls
Black Eye
Level: Probably Holdout
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: Skull marked with one eye.
Effect: Your shield does not charge normally. To charge your shields you must kill something (enemy or ally) with a melee attack (anything but the Energy Sword). You can charge your shields into the Overshield range by doing this.
Catch
Level: Probably The Storm
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: Skull marked with a stylized drawing of a plasma grenade.
Effect: AI will toss more grenades.
Famine
Level: Probably Refuge
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: Unclear
Effect: All weapons found on the ground have half ammo. Plasma weapons and lasers remain unaffected.
Fog
Level: Probably Cleansing
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: A skull marked with a swirl of fog
Effect: Unknown
Iron
Level: Probably Sierra 117
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: A skull marked with a stylized drawing of a hammer
Effect: When playing co-op, if either player dies the game restarts you at your last checkpoint. The effect resembles the effect already in place on legendary difficulty.
Mythic
Level: Probably Return
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: Unclear
Effect: Enemies have more health and shielding, and are therefore harder to kill. Exactly how much harder remains unknown.
Thunderstorm
Level: Probably Last Stand
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: A skull marked with a lightning bolt
Effect: All enemies are their most dangerous variant, although how this will be managed is currently unknown.
Tilt
Level: Probably The Key
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: Unclear
Effect: Unknown
Tough Luck
Level: Probably Tsavo Highway
Directions: Unknown
Difficulty: Probably Legendary
Achievement Icon: A skull marked with a three-leaf clover
Effect: Unknown
Background
While six of the skulls in Halo 3 have the same names as skulls in Halo 2, their effects may have been changed in some way, or as Bungie sees fit. For example, it is likely that the Mythic Skull still increases the difficulty of killing enemies, but it is not at all clear that it will do it in exactly the same ways as did Halo 2's Mythic Skull. Until Halo 3's release, little more can be said about the matter. Although it could be assumed that the Halo 2 names are actually placholder names.