Spoilers ahead; don't copy and paste if you don't want to know. You've been warned.

Note: None of the spoilers mention endings for Armageddon.
Liu Kang was killed at the beginning of Deadly Alliance as part of Shang Tsung and Quan Chi's plan to eliminate their greatest threat. Johnny Cage's fate has been retconned a couple of times. At first it was said he was killed and during Outworld's invasion (Mortal Kombat Trilogy) his soul rejoined his body and he lived on. Then it was suggested that when it was said he was killed, it referred to him being "killed" at the box office.
There has only been two Sub-Zeroes. The original Sub-Zero (MK1) was killed in revenge by Scorpion and entered the Netherrealm, where he was reborn as Noob Saibot and joined the Brotherhood of the Shadow, who worshipped Shinnok. Noob also found Smoke in the ruins of Shao Kahn's palace and reprogrammed him to join him during the events of Deception since he planned to use Smoke's nanotechnology to create his own army.
Since then, Smoke is back on his own.
The current Sub-Zero, the younger brother of the original, has been the Sub-Zero since MK2. The reason he returned unmasked in the original MK3 was to distinguish himself from his older brother but since then he's also donned a mask from time to time. He has also discovered that his family has descended from an Outworld race known as Cryomancers which explains his freezing ability. After Deadly Alliance, he discovered the armour of his ancestors which he wore as his main costume in Deception. As illini noted the design came out looking a lot like Shredder from TMNT.
illini wrote:4)does anyone even attempt to keep track of MK story lines anymore
It's difficult at times because they've retconned so many of the character's history and tournament outcomes but the storyline is still there and does make sense once it's pieced together. The thing is, with so many endings that conflict with one another you have to wait until a new game comes out so that you know which events are canon and which ones were just possible outcomes.