Never played MK1, but I'll say Sonya
MK2: Jax
MK3: Stryker
UMK3: Stryker
MK4: Sonya
MKDA Drahmin
MKD:Havik
MKA: Ermac
MKv.s.DCU: Sonya
MK2011: Stryker

MK1 - Sub-Zero.
MKII - Raiden.
(Never played MK3)
UMK3 - Shang Tsung. (I can be anyone! Muahahahaha!!)
MK4 - Shinnok.

MK:DA - Sub-Zero.
MK:D - Havik.
MK:A - My Kreated Fighter. (If not him, then Shao Kahn)

MK vs. DCU - Sub-Zero. (For DCU: The Joker)
MK 2011 - Cyber Sub-Zero.

mk1 - johnny cage

mk2 - johnny cage

mk3 - sub-zero

umk3 - human smoke

mkt - human smoke/johnny cage

mk4 - johnny cage

mkg - johnny cage

mkda - johnny cage

mkd - darrius/ noob smoke

mka - never played it

mkvsdcu - liu kang/ subby

mk2011 - johnny cage/smoke/cyber sub

MK1 - Sonya
MK2 - Mileena
MK3 - Sheeva
UMK3 - Mileena
MK4 - Tanya
MKDA - None
MKD - Mileena
MKA - Mileena
MK vs. DCU - None
MK2011 - Can't choose one

MK1-Sonya
MK2-Kitana
MKT-Sub-Zero
MK4-Tanya/Reiko
MKDA-Li Mei
MKD-Tanya/Kira/Li Mei
MKA-Sareena/Tanya/Li Mei/Khameleon
MKSM-Johnny Cage
MKDC-Kitana/Sonya/Flash
MK9-Mileena/Jade/Stryker/Ermac/Freddy/Smoke/Cyrax
This is for gameplay only

MK 1-Cage

MK 2-Cage

UMK 3- Reptile

MKT- Cage

MK 4- Cage

MKDA- Never played but probably Cage

MKD- Ermac and Sub-Zero

MKA- Everyone

MKvsDC- Sub-Zero

MK 9- Cage

MK1 - Sub-Zero

MK2 - Johnny Cage

MK3 - Kabal

UMK3 - Kabal

MK4 - Really?!

Didn't play Deadly Alliance, but I say Sub-Zero

MKD - Kabal

MKA - Shinnok

MKvsDCU - Scorpion/Sub-Zero tie

MK9 - Kabal/Noob Saibot/Ermac Tie ...oops, I meant !

mk1 sub-zero... mk2 kitana... mk3 kabal... umk3 noob saibot... mk 4 quan chi... mkda shang tsung... mkd mileena... mka rain... mk vs dc baraka... mk 9 sindel.

Of the ones I played:

MK - Sub-Zero

MKII - Shang Tsung

MK3 - Kabal

UMK3 - Robot Smoke

MKT - Noob Saibot

MK4 - Shinnok

MKDA - Shang Tsung

MKD - Baraka

MKA - Baraka

MK9 - Shang Tsung

Mortal Kombat: Scorpion

Mortal Kombat 2: Reptile/Mileena

Mortal Kombat 3: Sheeva/Kabal

Mortal Kombat 4: Kai

Mortal Kombat 5: Kenshi

Mortal Kombat 6: Ashrah

Mortal Kombat 7: ...

Mortal Kombat 9: Skarlet

MK1 - Kano
MK2 - Baraka
MK3 - Sheeva
UMK3 - Still Sheeva
MK4 - Shinnok
MKDA - Nitara
MKD - Baraka again
MKA - Yet again, Baraka
MK vs. DCU - Baraka for the 3rd time in a row
MK2011 - .....Baraka.

MK 1- Raiden
MK 2- Liu Kang
MK 3- Sub-Zero
UMK 3- Reptile
MKT - didn't play
MK 4/Gold - didn't play
MKDA - Reptile
MKD - Liu Kang
MKSM - Liu Kang (if this game counts)
MKA - Noob Saibot
MK vs DCU - Liu Kang (though I must note I hate this game and think it is crap)
MK 2011 - Reptile

MK2 - Mileena
MK3 - Sindel
UMK3/MKT - Mileena
MK4 - Tanya or Reiko
MKG - Tanya or Mileena
MK:DA - Kenshi
MK:TE - Sareena
MK:D - Kenshi or Mileena
MK:A - Kenshi or Sareena
MK vs DC - Sonya or Kitana
MK9 - Kenshi or Sonya

mk1-Kung lao
mk2-Shang tsung
mk3-sub zero
umk3-scorpion
mk4-havent played but i say johnny cage
mkda-(again)scorpion
mkd-shao khan
mka-Cyrax
mk9-kratos

MK1 - Scorpion (I'll give you a hint why... Toasty!)
MK2 - Kung Lao (The whole hat thing was awesome)
MK3 - Kitana (That's right!)
MKT - Kitana (I love the gal....)
MK4 - Johnny Cage (The ending won me over)
MK DA - Kung Lao (Hat lodged into skull, removed in style NUFF SAID)
MKD - Tanya (I love me some body part removal)
MKA - Kung Lao (Yeah him again)
MKVDC - Kitana (It really wasn't difficult)
MK9 - Kung Lao (Problem?
Yeah I'm a huge Kung Lao/Kitana fan.

MK1 - Sub-Zero
MK2 - Sub-Zero/Cage
MK3 - Stryker/Cyrax
MK4 - Sub-Zero
MKDA - Kenshi/Sub-Zero/Cyrax
MKD - Kenshi/Darrius
MKA - Kenshi/Cyrax
MK vs. DCU - Sonya
MK9 - Cyrax, Kenshi

I generally have more than one favourite in each game.

Mortal Kombat: Kano.
Mortal Kombat II: Shang Tsung.
Mortal Kombat III: Kano.
Mortal Kombat Trilogy: Khameleon (I Guess).
Mortal Kombat Gold: Jarek.
Mortal Kombat Deadly Alliance: Frost.
Mortal Kombat Unchained: Frost.
Mortal Kombat Armageddon: Frost, Moloch, Daegon.
Mortal Kombat vs DC Universe: All DC Characters.
Mortal Kombat 2011: Freddy Krueger.

MK1 - Jonny Cage
MK2 - Baraka
MK3 etc - Stryker
MK4 - Reiko
MKDA - Kenshi
MKD - Havik
MKA - Didn't Realy like any of the new characters
MKvsDC - Superman
MK2011 - Skarlett since shes the only new character.

I just picked from the characters introduced in each game, Otherwise it would have been Jonny Cage most of the time.