Okay. Here's a quick rundown, based on all the info I've seen, for those who may be confused:

Ashrah - Active
Baraka - Active
Ben/Kobra - Active
Blaze - Unknown
Bo' Rai Cho - Active
Chameleon - Unknown
Cyrax - Unknown
Dairou - Active
Damashi - Active
Darrius - Active
Dragon King - Active
Drahmin - Imprisoned
Ermac - Active
Fujin - Imprisoned
Frost - Unknown, presumed alive (listed as friend in Sub-Zero's bio)
Goro - Dead
Havik - Active
Hotaru - Active
Hsu Hao - Imprisoned
Jade - Imprisoned/Active O_o
Jarek - Imprisoned
Jax - Unknown
Johnny Cage - Unknown
Kabal - Active
Kai - Unknown
Kano - Unknown
Kenshi - Active
Khameleon - Unknown
Kintaro - Unknown, presumed dead
Kira - Active
Kitana - Imprisoned
Kung Lao - Unknown
Li Mei - Active
Liu Kang - Active Undead
Mavado - Unknown
Mileena - Active
Moloch - Unknown
Motaro - Dead
Nightwolf - Active
Nitara - Unknown
Noob Saibot - Active
Onaga - Active
Quan Chi - Unknown
Raiden - Active
Rain - Unknown
Reiko - Imprisoned
Reptile - Matter of great debate
Shujinko - Active
Sareena - Unknown
Scorpion - Dead :D
Sektor - Unknown
Shang Tsung - Possibly Alive (seen in backgrounds)
Shao Kahn - Inactive, but Alive (Confirmed by Midway)
Sheeva - Dead
Shinnok - Unknown, presumed Dead
Sindel - Active
Skab - Active
Smoke - Active
Sonya - Unknown
Stryker - Imprisoned
Sub-Zero (Elder) - Dead
Sub-Zero (Younger) - Alive
Tanya - Active

(Note: Mokap and Meat are not counted as actual characters. Reptile's status is to be avoided for now, to prevent flame wars, and here we assume that Onaga,and Havik are unique characters)

If I've left anyone terribly important out or made a serious error, tell me.