LP - Low Punch
LK - Low Kick
HP - High Punch
HK - High Kick
BLK - Block

Note: It is best to hold BLK when performing moves that involve the up command that is not at the end of the move to stay grounded.
 
Note 2: All fatalities are done up close unless noted. To do the acid fatality, hold LP + LK when doing the uppercut.
 
Note: 3: To perform a Babality or Friendship, you must not use punches during the decisive round. 

Note 4: You may also notice that some button holding fatalities last longer the Fatality allotted time so you must hold the button during the fight such as Shang Tsung's Kintaro fatality which you must hold LP for 25 seconds and release.

Lui Kang
Fireball: f, f + HP
Low Fireball: f, f + LP
Flying Kick: f, f + HK
Bicycle Kick: Hold LK for a few secons and release
 
Fatality 1: 360 away from opponent 
Fatality 2: d, f, b, b + HK
Friendship: f, b, b, b + LK [disco time]
Babality: d, d, f, b + LK
Pit Fatality: b, f, f + LK
 
Kung Lao
Hat Toss: b,f + LP (aim with u or d)
Teleport: d, u
Lunging Kick: d + HK in air
Spinning Tornado: u, u (Press LK for more spins)
 
Fatality 1: f,f,f + LK within sweep range
Fatality 2: Hold LP, b, f (press u near the head to decap)
Friendship: b, b, b, d + HK (pull a rabbit out of the hat)
Babality: b, b, f, f + HK
Pit Fatality: f, f, f + HP

Johnny Cage
High Fireball: d, b + HP
Low Fireball: d, f + LP
Shadow Kick: b, f + LK
Shadow Uppercut: b, d, b + HP
Split Punch: LP + BLK
 
Fatality 1: d, d, f, f + LP
Fatality 2: f, f, d, u (d + LP + LK + BLK to do three in a row)
Friendship: d, d, d, d + HK (autograph please)
Babality: b, b, b + HK
Pit Fatality: d, d, d + HK
 
Reptile
Acid Spit: f, f + LP
Slide: b + LK + HK
Invisibility: u, u, d + HP
Force ball: b, b + LP + HP
 
Fatality 1: b, b, d + LP from a jump away
Fatality 2: f, f, d, HK while invisible
Friendship: b, b, d + LK (buy a Reptile doll)
Babality: d, d, b, b + LK
Pit Fatality: d, d, f, f + BLK
 
Sub Zero
Freeze: d, f + LP
Freeze Ground: d, b + LK
Slide: b + LK + HK
 
Fatality 1: f, f, d + HK from a sweep away then f, d, f, f + HP
Fatality 2: Hold LP, b, b, d, f, release LP from a full screen distance
Friendship: b, b, d + HK (buy a Sub Zero doll)
Babality: d, b, b + HK
Pit Fatality: d, f, f + BLK
 
Shang Tsung
Flame Skull: b, b + HP
2 Flame Skulls: b, b, f + HP
3 Flame Skulls: b, b, f, f + HP
Lui Kang Transformation: b, f, f + BLK
Kung Lao Transformation: b, d, b + HK
Johnny Cage Transformation: b, b, d + LP
Reptile Transformation: u, d + HP
Sub Zero Transformation: f, d, f + HP
Kitana Transformation: BLK, BLK, BLK
Jax Transformation: d, f, b + HK
Mileena Transformation: Hold HP for 2 seconds and release
Baraka Transformation: d, d + LK
Scorpion Transformation: u, u
Rayden Transformation: d, b, f + LK
 
Fatality 1: u, d, u + LK
Fatality 2: Hold HK then release from a sweep distance away.
Fatality 3: Hold LP for 25 seconds
Friendship: b, b, d, f + HK (rainbow)
Babality: b, f, d + HK
Pit Fatality: d, d, u, d
 
Kitana
Fan Toss: f, f + LP + HP
Fan Lift: b, b, b + HP
Slicing Fan: b + HP
Square Wave Punch: f, d, b + HP
 
Fatality 1: BLK, BLK, BLK, HK
Fatality 2: Hold LK, f, f, d, f, release LK
Friendship: d, d, d, u + LK (let there be cake)
Babality: d, d, d + LK
Pit Fatality: f, d, f + HK
 
Jax
Slamathon: rapidly press HP during throw
Gotcha Grab: f, f, rapidly press LP
Ground Pound: Hold LK for three seconds and release
Hammerfist: f + HP
Energy Boom: f, d, b + HL
Backbreaker: BLK in air
 
Fatality 1: BLK, BLK, BLK, BLK, LP within sweep range
Fatality 2: Hold LP, f, f, f, release LP within sweep range
Friendship: d, d, u, u + LK (paper dolls)
Babality: d, u, d, u + LK
Pit Fatality: u, u, d + LK
  
Mileena
Sai Toss: Hold HP for two seconds and release
Teleport Kick: f, f + LK
Roll: b, b, d + HK
 
Fatality 1: f, b, f + LP
Fatality 2: Hold HK for three seconds and release
Friendship: d, d, d, u + HK (a flower grows)
Babality: d, d, d + HK
Pit Fatality: f, d, f + LK
 
Baraka
Blade Beam: d, b + HP
Blade Swipe: b + HP
Slice n Dice: b, b + LP
 
Fatality 1: b, f, d, f + LP
Fatality 2: b, b, b, b + HP from a jump distance (start from sweep distance)
Friendship: u, f, f + HK (I got a present for you)
Babality: f, f, f + HK
Pit Fatality: f, f, d + HK
 
Scorpion
Spear: b, b + LP
Teleport Punch: d, b + HP
Leg Takedown: f, d, b + LK
Air Throw: BLK in air
 
Fatality 1: Hold HP, f, d, f, f, f, release HP
Fatality 2: u, u + HP from a jump distance
Fatality 3: d, d, u, u + HP
Friendship: b, b, d + HK (buy a Scorpion doll)
Babality: d, b, b + HK
Pit Fatality: d, f, f + BLK
  
Raiden
Lightning Bolt: d, f + HP
Superman: b, b, f
Teleport: d, u
Shock Therapy: Hold HP three seconds and release
 
Fatality 1: Hold LK five seconds and release then press LK + BLK rapidly
Fatality 2:Hold HP seven seconds and release
Friendship: d, b, f + HK (Kidd Thunder)
Babality: d, d, u + HK
Pit Fatality: u, u, u + HP
 

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There are three secret characters you can face but one of them is easier to fight on the console than on the arcade.
 
Jade: Make it to the match before the question mark and defeat your opponent using only the LK button
 
Smoke: Get to the portal room and use an uppercut to trigger Dan Forden's Toasty and press d + Start

Noob Saibot: Win 50 matches in a row in vs. fighting.

Azul Fria : this guide seems to be really helpful. If I happen to ever play this game I'll definitely have to look at this guide because when it comes to old school fighting games, I suck LOL. Great job on this guide.

If I was to play this game, this guide would probably be very helpful to me especially starting off in the game. Great guide, I hope to see more guides from you in the future.