If you play in two player mode you'll notice that there are 6 skulls on the bottom of the loading screen. When you press player one's low punch key the first skull will change to 1 if you press it again it will change to 2 etc. The second skull will change if you press block, the third will change if you press low kick. For the fourth, fifth and the sixth skull you have to do the same thing with player two's keys. Type in the following combinations for special effects:

111-111 Random free weapon
555-555 Many free weapons
222-222 Start with random weapon
100-100 Disable throws
010-010 Disable maximum damage
110-110 Disable throws and max damage
444-444 Start with weapons drawn
666-666 Turn off music
050-050 Exploding looser
123-123 One hit win
060-060 No rain on Wind World
020-020 Red rain on Wind World
002-002 Players don't drop weapons
012-012 Noob Saibot Mode - must beat the game with Reiko first
001-001 Unlimited Run
321-321 Big head mode

Stage Select

011-011 Goro's Lair
022-022 The Well
033-033 Elder Gods
044-044 The Tomb
055-055 Wind World
066-066 Reptile's Lair
101-101 Shaolin Temple
202-202 Living Forest
303-303 The Prison
313-313 Ice Pit