Halo 3 skulls

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.

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.