My fave that I've heard so far from either movie is this one that was in the script for MK1:

Scripted but not filmed was a scene where Shang Tsung allowed the earthrealm combatants a night to bury and mourn the loss of Art Lean. They buried him the garden of statues, underneath a statue of the Great Kung Lao.

It would have been the only place where Lao appeared in any form in either of the movies (although he is mentioned twice in MK1 by Shang and Liu) , and would have been fuckin awesome
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But speaking of scenes that never were, I always thought this would have been a much better part of the ending fight scene:

When Shang revives like 10 crap fighters, and Liu beats their asses - they could have had Shang Tsung MORPH into the Great Kung Lao (cus he has his soul u know) and fought Liu in a kick-ass battle...

I just found another 'cut' scene from MK1, but this one was actualy filmed:

An HBO "first look" program showed an alternative death for Scorpion. Instead of exploding after the shield slice, he falls off a platform and onto a spike in an emulation of the classic pit death scene from the video game series.

(I like this thread topic)

I heard that at the end of MKA Quan Chi was supposed to make an appearance. I know someone could elaborate on this a little more.

Oh I can...

Along with probably hours of unused fight scene footage, there have also been reports of a completely alternate ending to the film, where Shinnok is seen in the Netherealm talking to Quan Chi, who is otherwise not seen in MKA. All the ending consists of is; Shinnok asking if everything is going according to plan, Quan Chi nods yes, and they both leave.
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I remembered two other scenes that were rumored (the 1st definately being possible) from the 1st MK movie:

1) In the scene at dinner where Shang's minions clear all the tables out of the way and knock the food on the floor for Sub Zero to fight in the 'taste of things to come' scene - it was rumored / was orginaly planned for Scorpion fight too. If u watch when the minions are being led out Sub Zero AND Scorpion are at the front of the lines. After that they all turn, Scorpion can be seen once again a bit further down the line now. And then he is not seen again until his fight w/ Johnny Cage. Where did he go? When the movie was orignaly written / planned it was going to be an 'R' film, and I've heard Scorp was goin to impale someone (one of those minions probably) w/ his spear.

2) In the released movie, in that same scene, Sub Zero freezes the guy and he shatters. But in the 'R' planned movie, he was to freeze the opponent and perform his head-rip fatality. (I'm not 100% sure this one is true, but it is possible that it was going to be part of the movie when it was going to be an 'R')

So when they changed it to a Pg-13 to generate more revenue, they cut more of the gory, game-like scenes

Hopefully some day us MK fans will finally get to see ALL of these deleted scenes from the first films. Our best chance is to hope that when MK3 is released they are kind enough to put in at least half of thse scenes on to DVD.

Here is alink where you can see the Quan Chi alternate ending scenes and also what seems to be a Goro deleted scene.

Enjoy http://www.mortalkombat.com/film-downloads.shtml

I was wrong about what I said above so please ignore it.