At the end of the level, face the Pelican that arrives. Don't get on it. Turn 90 degrees to the left and jump onto the large ledge. Walk all the way down until you see another (thinner) ledge on the building in front of you. Jump onto it and follow it all the way to the end where the Skull sits in the shadows.
Effect: In co-op games, if one player dies, you all restart at the last checkpoint. In individual games, if you die, the entire mission restarts.
Black Eye
Black Eye Skull - Crow's Nest
At the start, there is a massive pipe above you with the skull on top. Walk up the two small stairs and on the left there's some shelves you can jump on to. Jump up to the metal bars and then onto the pipe. Continue to the end where you'll see a Skull. Plus, you don't have to use the RB button to pick this one up.
Effect: The only way you can recharge your shields is by landing melee attacks on your opponents.
Tough Luck
Tough Luck Skull - Tsavo Highway
This skull is located after you go through the shield that blocks the road. (After you hear the guy on the radio request help.) You'll exit onto a bridge with a large pipe on your left. Climb up one of the yellow ladders and turn right. Continue down and jump over the yellow guard thing that blocks your way. Immediately turn left and jump all the way down on the grey support below. Walk down the support and look left, you'll see a ledge coming out of the cliff. On the ledge is the Skull.
Catch
Catch Skull - The Storm
From the start continue through the level until you're outside. Grab a vehicle and kill the enemies such as the grunts and other small enemies. DO NOT DESTROY BOTH WRAITHS. Destroying or kicking the drivers out of both Wraiths will cause the skull to disappear. Best way to do it, take out the one with the Flak Cannon batteries atop the one on the ground. Then go to the top right corner on the plains where there is some sort of small silo tower. The Skull is sitting on top. To get to the skull: Grenade jump up, or if that doesn’t get you high enough park a vehicle by it and use that for extra lift. This needs to be done near the front of the building. (To grenade jump, face where you want to go, then throw a grenade just in front of your feet, then run and jump towards your desired location. Be sure to duck down near the peak of your jump to get that last little bit of height. The explosion beneath will give you extra lift and hopefully not kill you!)
Effect: Enemy units will throw grenades at an alarming rate - Roger Clemens style.
Fog
Fog Skull - Floodgate
At the very start of the level, as you walk up the stairs leading into the town (the marines will start talking), look up and to the right to the first building on your right (past the missile turret). A single Flood will appear and then jump across, and out the map. Shoot him before he jumps and the Skull will fly down to the ground. However, if you shoot him too early the Skull will land on the roof and you will have to try again. Do not mistake him for the two Flood that jump onto the roof of the building directly ahead.
Effect: Your radar is disabled.
Famine
Famine Skull - The Ark
This skull is located after you get the Mongoose and drive over some small cliffs. Then you have a choice: straight on or turn right. (Either way you have to go down the right path later.) Continue down the path and defeat the Ghosts that attack you, under a big "metal cover thing." Then, after coming out from under the big "metal cover thing", turn right to go up a path leading to some enemies and a small cave/tunnel. Instead, stop on the path, and look right to see a bolder jutting out of the rock. Hop on the top of the bolder and up onto the rock. Then jump over onto the top of the big "metal cover thing" (mentioned earlier). Turn left and walk up to the last support that juts out the Skull is at the end of it. This next bit can be a bit tricky. Using a grenade, grenade jump forwards and onto the support. Pick up the Skull. (To grenade jump first face where you want to go, then throw a grenade just in front of your feet, then run and jump towards your desired location. The explosion beneath will give you extra lift and hopefully not kill you!) Alternatively, if you don’t want to attempt grenade jumping you can use the 'Deployable Cover' equipment right by the edge of the support. If you place it in the right position you can jump onto the support beam easily from there and grab the skull
Effect: When enemies drop their weapons, they will have considerably less ammo in them.
Effect: All of your enemies will dive with incredible success away from your grenades, plasma pistol bolts, needles and vehicle splatter attempts
Thunderstorm
Thunderstorm Skull - The Covenant
This skull is located on the second tower. After shutting down the first tower, grab the hornet and fly over to the second tower. Once you land, head up the staircases as if you were going to the entrance, but just before look towards the centre to see the dividing staircase that leads to a platform. Walk to the end, and the Skull is on the ground.
Effect: Each enemy receives a field promotion and is upgraded to their next available level.
Tilt
Tilt Skull - Cortana
Continue through the level until you drop down into an open, fleshy hole, into a small room with an open door and an Energy Sword beside a dead Elite to the right. In the next room is a circular floor. Walk straight in (kill the flood first) to the middle of the platform and turn left 90 degrees. You should see two small ramps leading downwards. Hop on to the divider of the ramps and up onto the "mushroom like" platform coming out of the wall to your left. (Cortana will say some weird stuff about playing games.) Then jump again onto the next platform just above you. Turn around 180 and look up, jump to the next platform and run across the fleshy pipe onto, a bigger, purple platform. Sitting in the centre, in a puddle of bones and fluid, is the Skull.
Effect: Enemy resistances are greatly increased. For example, the Brute power armor is normally pretty resistant to human weapons to begin with and fairly fragile against plasma shots. With Tilt turned on, The Brute armor is practically 100% resistant to any human projectiles and can only be taken down by plasma bursts.
Mythic
Mythic Skull - Halo
This Skull is at the beginning of the level. Head into the cave in front of you, straight away keep to the right, and there is a small path that leads off to some rocks. The skull is sitting in front of them.
Effect: Every enemy on the field now has double their normal amount of health.
Blind
Blind Skull You lose your HUD when this skull is turned on. You wont see your weapons, shield, radar, etc. Location: The Blind Skull is the first of the Silver Skulls in Halo 3, and can be found in the first mission. It is located relatively close to the beginning of the level.
After your first encounter with the Gold Armor Brute, Two enemy dropships will appear a bit further down the stream. Go towards the dropship that is furthest away, and stay on the right side of the stream. Continue along the right (towards the cliff edge), and a rock will jut out a bit over the large lake. The Blind Skull is located on this rock.
Grunt Birthday
Grunt Birthday Party Skull When you get a headshot on an enemy Grunt, they will explode into confetti, and you�ll hear children cheer, �Yay!� in excitement. Location: This is one of the more fun Silver Skulls in Halo 3. The Grunt Birthday Party Skull is located on the second mission, Crow"s Nest, just before the area where you team up with the Arbiter (it"s the piping area where you see Drones buzzing in and out of an array of pipes). Just before you jump down the pipe to meet up with the Arbiter, stop at the ledge, and look directly below you. Along the wall that you drop down, there is a small ledge with a green arrow pointing backwards. Jump onto this ledge (rather than all the way down), and go inside this secret room. The skull is in the dead center of the room.
Cowbell
Cowbell Skull Explosions become much bigger in the game. Location: The Cowbell Skull is found on the level The Ark, and marks the third Silver Skull found in the game. It"s fairly far into the level, so it takes a bit of time to find it. Begin by heading all the way to the part of the level where you battle the Scarab. After defeating it, look in the middle of the desert area which you battled it in for a fairly large structure (it's the building you see if you are at the bottom of the ramp you are supposed to go up, and turn to look in the opposite direction). Inside of this structure are several Gravity Lifts (shown below). Take one of these for later.
Next, head up the huge ramp, and head inside of the building (the one with the cartographer inside). Pass through a few of the rooms in this building, and you�ll eventually come to a room with a whole lot of Explosive crates. Right after this room is a Staircase/Hallway that leads to the level below. The Skull is located at the top of the room, at the point where you turn on the staircase to head for the next part of the slope. There are four platforms above you, the Skull is on the uppermost of these platforms. Use the Gravity Lift to jump up to it, and there you have it!
IWHBYD
IWHBYD Skull
Unlocks hidden dialogue throughout Halo 3's campaign.
Location:
The IWHBYD Skull has been found! After countless hours from the Halo3Planet Community, we finally present you with the location of the final skull, the IWHBYD Skull!
The Skull is located in the level, The Covenant. After defeating the Scarabs, and going inside, get to the location with all 7 Ring Holograms. You must jump through the rings in a specific order. That order is as follows (1 is at the entrance, 7 is at the end):
E F# G F# A G F# E B C# D C# A C# B D E G A F# E G F# E F# D E
After jumping through them in this sequence, you will be awarded the �I Would Have Been Your Daddy Skull�. It will be right next to the bridge that brings you over to the Prophet of Truth.
NOTE: YOU MAY NEED TO KILL THE PROPHET OF TRUTH, AND THE FLOOD BEFORE DOING THE RING JUMPS!
* You can get the skull on Normal, Heroic, or Legendary.
* No skulls have to be active
* You can work as a team, have one person jump through a ring then another, provided they are in the correct order. This will speed things up for you.
Iron Skull - Sierra 117
Black Eye Skull - Crow's Nest
Tough Luck Skull - Tsavo Highway 
Catch Skull - The Storm
Fog Skull - Floodgate
Famine Skull - The Ark
Thunderstorm Skull - The Covenant
Tilt Skull - Cortana
Mythic Skull - Halo
Blind Skull
Grunt Birthday Party Skull
Cowbell Skull
IWHBYD Skull