"Puff levels" refer to how puffy John's hair is at any given time. Puff levels increase due to natural hair growth, stress, and, in rare cases, excitement. Also important to note is that you do not choose the puff, the puff chooses you.

Interesting note: During John's paternity leave, WheezyWaiter created a video intended to emulate John's videos in as many ways as possible. One method was "trying to raise the puff levels" in his hair, but he ceased this on the grounds that he "didn't have very much and was afraid if he kept doing this he'd go bald permanantly."

A Nerdfighter made a parody called "The John Green Puff Index," a parody of the World Suck Index. If you search "John Green Puff Index" on Google, it should come up.

CrashCourse made a puff level meter in the World History episode The Crusades - Pilgrimage or Holy War?: Crash Course World History #15 at 7:25