Sektor, Cyrax, and Smoke are references to the Predator series. (Their looks, Cyrax's self-destruct fatality)

Kano's Metal Eye is a reference to the Terminator

Lui Kang's character was a refrence to Bruce Lee (gretest martial artist!)

The Black Dragon Clan was based on a secret communist Japanese group named the Kokuryu Kai, i think, that existed during the World War 2 era.

The Lin Kuei clan is based on a true chinese Lin Kuei sect of thieves/ warriors/ assassins, that may have spawned what today we call 'japanese shinobi' (ninja).

Kung Lao's hat is a reference to that fat bastard with a razor sharped edged hat in an old 007 James Bond film.

Kobra was firstly named Ken, wich may be a reference to Capcom's Street Fighter character, if you notice the resemblance between the two of them.

"Bo Rai Cho" can be translated to Spanish, forming the word "borracho", wich means "drunk" in english.

Sheeva's name may or may not, be a reference to that eight armed (?) divinity (goddess?) from Thai culture.

Oddjob and Shiva

Shujinko is reference to some old guy
Shao Kahn's name may be reference to Gehngis Kahn, some mongolian guy who tried to take over places a long, long time ago

Probably Pai Mei from Kill Bill Volume 2, or at least old Japanese/Chinese masters of fighting.