Cooldown is the interval of time between attacks.
Factors affecting cooldown include the power and range of an attack. As a general rule, the more powerful an attack the longer it takes to attack again. Melee units such as Zerglings are much faster than a ranged unit like Siege Tanks. Another example would be the Marine's gauss rifle firing much faster than a Dark Templar slashing with its Warp blade.
Special abilities are not affected by cooldown limitations. However, they can affect the cooldown of other units such as the Queen's Ensnare spell.
For more information see Cooldown on the parent site.