Khan sites feature Captain Kirk's "KHAAAAAAAAN" scream from Star Trek II: The Wrath of KHAN. The original site  pre-dates YTMND; it was found on the /contrib page of the original yourethemannowdog.com. However, its popularity carried over, and the scream became a staple of early-era YTMND.
Khan! was the first major fad on YTMND, sparking hundreds upon hundreds of imitators, and setting the precedent for fad or spin-off sites of notable YTMNDs.
Most recently, members of the "Forgot Poland" Army started making "KHANTMND" sites that mix the most popular sites with the Khan scream. It is done the way many Poland sites are done, but is much less popular.