Probably my favourite ever is Kung Lao's MK Gold ending, it's too bad he and Goro didn't actually fight.

MKMSZ's ending owns too, when Shang invites SZ to compete in MK1.

Oh, and the secret win screen when you beat MK3 on the most difficult tower.

Other good ones:

MKDA:

Quan Chi

MK4:
Kai
Tanya
Raiden

MKT:

MK1 Kano (Cus it's set in half of the "Palace Gates" stage, which of course, doesn't appear in the game itself.)

MK1:

Kano ("Battle of the Sans")

Noob Saibot- MKD (shocking imo)
Sub-Zero- MK2
Kitana- MK2
Tanya- MK4/G

Scorpion- MKDA
Sub-Zero- MKD

Definitely definitely DEFINITELY blaze from MKDA...

after he broke free..he carried on doing whatever he was doing before he was captured....

mine would be subzero mk4

MKD Hotaru

MKDA Shang Tsung, Bo' Rai Cho, Scorpion

MK3 - Smoke, Shang Tsung,

MK1- Raiden

those are cool