There are a total of 13 gold and silver skulls throughout the game. They unlock various challenges (no hud, enemies invulnerable to human weapons, etc.) The gold skulls also unlock achievements and have a point bonus multiplier. This is handy for unlocking the 15,000 point and 50,000 point achievements. Furthermore, to get the Hayabusa armor, you must gather all 13 skulls, then unlock 1`,000 achievement points (aka ALL of them) to get the 4th piece of the Hayabusa suit... a KATANA.
...no, you can't use it, but it looks frigging sweet in multiplayer.
go to
http://www.zimbio.com search "halo 3 skulls" to find out everything you need to know.