Remember: All Skulls must be found by setting the game to “Normal” difficulty setting or higher, and you must begin from the start of the level to find them!
Gold Skulls:

1. Iron Skull
2. Black Eye Skull
3. Tough Luck Skull
4. Catch Skull
5. Fog Skull
6. Famine Skull
7. Thunderstorm Skull
8. Tilt Skull
9. Mythic Skull

Silver Skulls:

1. Blind Skull
2. Grunt Birthday Party Skull
3. Cowbell Skull
4. IWHBYD Skull

And then there is the Unknown Skull, which is neither silver or gold, and has no effect that we have seen.
About Skulls in Halo 3
Skulls were first introduced in Halo 2, where picking up a hidden skull in the “Legendary” game difficulty would create an undesirable effect against the player (such as not being able to see anything on their HUD). In Halo 3, skulls can be found scattered throughout the levels on Normal, Heroic, and Legendary difficulty settings. Picking up “Golden” skulls will also unlock an achievement on the Xbox 360. After picking up a skull in the game, you can enable the skull’s effects in Meta Games, which will in turn multiply your meta game score.
Overall, Skulls can make for a very interesting play experience, and really help to show who is the Master of the game through meta game scores.