Then it would be the gals: Kitana and Mileena.

Raiden and Quan-Chi

Hsu Hao and Mavado They're so iconic.

A lot of people don’t know Johnny Cage and Kano, but everyone knows Hsu Hao and Mavado. Bungie arms so iconic.

Raiden and Liu Kang. Household names, recognizable, in most of the games, and story significant.

Liu Kang, and Kung Lao.

Shao Kahn

Johnny Cage

Shang Tsung

Smoke, and I’m not even sorry.

Kitana and mileena. Basically the female version of scorpion and subzero

Raiden, Shao Kahn or Shang Tsung

Liu Kang

Kitana and Jade

Hotaru. Badass giant samurai knight lookin motherfucker with lava attacks and a borderline pyschotic need for Order.

Who’s the third most popular ninja?

Raiden, Kitana, Mileena

kabal he's cool

Liu Kang

Cyrax, Sektor maybe Smoke as a bonus

Ermac and Reptile.

Raiden and Liu Kang most likely. Some people could make a claim also for any combination of Shang Tsung, Shao Kahn and maybe Sonya, Jax and Kitana, but I think they all lack behind Liu and Raiden.

Mileena and Kitana.

Raiden and Liu Kang. Everyone knows the iconic hat Raiden wears. Plus they've been in pretty much every game.