The best perks in Call of Duty: Ghosts are those that give you more damage, help you stay hidden and give you an advantage in contested firefights.
Deadeye is the Stopping Power of Call of Duty: Ghosts. It has a chance to give you 40% more bullet damage depending on your current killstreak. On any weapon were Deadeye reduces the number of bullets it takes to kill somebody it gives you a massive davantage over enemies. Snipers and shotguns benefit the least from Deadeye.
In Call of Duty: Ghosts hearing enemies’ footsteps is very easy. It gives you the most valuable information in any FPS: the position of enemies. Thus you need to ensure that your footsteps can’t be heard in all classes were you will spend any time close to enemies, that is any class other than snipers. Therefore use Dead Silence on those classes. Note that Amplify isn’t that reliable, especially when enemies equip Dead Silence which is fairly common.
The last perk that is essential for all classes in Call of Duty: Ghosts is Focus. It reduces flinching which is often the reason you lose a contested engagement. Even on shotguns, where you usually should fire from the hip, Focus is important.