From Final Fantasy Wiki

A nunchaku is a recurring weapon in the Final Fantasy series that appear as pair of sticks joined together by a chain or rope.

Appearences

Final Fantasy

Nunchucks appear in the original Final Fantasy as weapons for Black Belts. However, due to how barehand damage is calculated, it is usually better for Monks to avoid using them at all.

Final Fantasy III

At least two or three types of nunchaku are available in the beginning of the game as a weapon for Monks and Black Belts.

Dirge of Cerberus -Final Fantasy VII-

Shelke the Transparent uses EM Sabers that are attached to a rope, similar to a nunchaku though they closely resemble lightsabers.

Final Fantasy VIII

Selphie Tilmitt uses an over-sized nunchaku as her weapon of choice. Her weapons include Flail, Morning Star, Crescent Wish, and Strange Vision.

Final Fantasy XIII

Oerba Yun Fang wields a spear that can turn into a three-section-staff, a weapon similar to a nunchaku expect with three sticks instead of two.

Trivia

• Fighter McWarrior from the webcomic 8-Bit Theater often makes jokes about putting nunchucks and swords together to form the "Sword-chucks". Though the idea was at first ridiculed by his peers, Fighter successfully used them to do battle against Kary, the Fiend of Fire.
• In another joke, the weapon shop owner for the first town mentions he only has nunchucks for sale. When Red Mage asks why nunchucks, an eastern weapon, are being used in a western-medieval style setting, the owner replies "why do you think I still got a whole crate of them?"