To quote MK Secrets:

Kommand Prompt Kodes:
To use one of these codes, put it as an argument to mk3 when you run mk3.exe For example, instead of just typing "mk3" to run the game, type "mk3 666" You can combine codes too. "mk3 666 1995" If possible, the official name of the code is listed in all caps.

666 - Smoke Enabled
0666 - Smoke Enabled and CPU is harder
1000000 - Shao and Motaro Enabled in 2 player mode
831 - Noob Saibot Mode (shadow mode)
1995 - Invisibility Mode
8000 - Turbo Mode
603015 - Slow-motion Mode
4862222 - Block is Bad (when you block most of your energy will be lost)
9966 - Mirror Mode
1111 - Floating Mini-people Mode
54321 - Miniature Mode
12345 - Giant Mode
8888 - Fat Mode
NOBLOOD - Turns off blood until you turn it back on.
BLOOD - Turns blood back on.
NOVIOLENCE - Turns off fatalities until you turn it back on.
VIOLENCE - Turns on fatalities. Blood must also be on for fatalities to work.

I can't get a single one of these damn things to work. Anyone have any idea as to how to do this with dosbox?

EDIT: FINALLY got them to work. Edit the configs without a dash in the numbers.