There are alot of different ways for a mod to track and display cooldowns.
Most of these have tons more available features, click a link for more information!
ForteXorcist: Look at the "cooldown timer". It is popular because of the unique and compact logarithmic single bar timer.
Ghost Pulse: Flashes the spell in question's icon at a larger scale quickly to alert the user upon a cooldown's completion.
MSBT: Scrolling combat text mods generally contain textual cooldown alerts. They do have more than just that though.
Power Auras: Gives visual queues for buffs, debuffs, cooldowns, and many others. It doesn't flash the spell icon like Ghost Pulse does, instead it display images or text that you can see through the link.
Cooldown Buttons: Cooldowns displayed in buttons (cyCircled & ButtonFacade compatible) and optional text alerts.
Omnicc: Puts the time of the cooldown on the spell/item in question. It can also can flash the icon when the spell is available to use again. It is very simple but a must have.
Cooldown Watch: Bar format for your cooldowns.
rFilter2: Zork's small debuff timer, you need to edit the lua (code) to customize it for your class, not for most users.