There are characters who are added in and confirmed non-canon -- for example, the addition of "Classic Sub-Zero", whom we now know to be Noob Saibot, as well as MK1 and 2 bosses, and MK1 versions of Kano, Raiden, etc.

Another example is characters who are added in but given no storyline -- Meat, Chameleon (the male ninja, not the female Khameleon), and, at the time of MK2, even Noob Saibot, Smoke, and Jade.

However, most character additions are both relevant and canon. Jade, Reptile, and Kitana's UMK3 story most certainly did happen. Cyrax's ending in MKG is necessary to the storyline of MK:DA. Even Mokap and Blaze are most likely canon.

It can be tricky to figure out what did and didn't happen in MK games, but as long as the character is given a story, it's safe to assume that they were some part of the events that occurred (with rare exceptions occurring, as in Classic Sub-Zero.)

I think the Non-canon characters go as follows:

UMK3-MKT: Human Smoke. His UMK3 endingm which was retconned because it was silly, states he does no longer actually exists as a human.

MKT: Kintaro, Goro: Only there for completion. No endings whatsoever.

MK4/G: Meat. No story.

My P.O.V on others:

Masked Sub-Zero: Noob Saibot.

Chameleon (M) is tricky. When you choose to fight him upon completing the game, he is referred to as one of Kahn's warriors. So I assume him to have existed, but wasn't really relevant to the plotline. Probably killed in the war.

As for the MKI and II versions of the characters...well, who's to say they didn't just change clothes during the war? Doesn't really matter...I think their endings were the same as their counterparts.

Some people say Goro's MK4 appearance isn't canon....but, his bio says he's out for a Rematch with Liu Kang. So that's that

If I remember right, there's even some debate as to whether or not Sektor's MKG appearance is canon, since MKDA retcons Cyrax's MK4storyline, claiming the Special Forces found him instead of the Lin kuei, which negates Sektor's storyline of being sent to keep an eye on Cyrax. I basically look at it as being that Sektor is sent to find Cyrax instead. His ending, in that case, would still make sense (even if it didn't happen).

And, of course, there's the ever present debate over whether Reiko's ending happened and is he Shao Kahn and blah blah blah... it can be very exhausting to keep up with. Gavok's Mortal Kombat Story FAQ is very helpful in keeping track of it all. It can be found at the Kombat Pavilion (check Network), GameFAQS, and any number of other places.

As for Sektor/Cyrax/USSF/MKG, I tend to side with the MKG explanation of things. Given the way MK4/G were totally neglected throughout MK:DA Konquest, it seems like the writers in charge of Konquest just plumb forgot how Cyrax ended up with the Special Forces and created a reasonable explanation. It's a moot point anyhow.

And on an unrelated note, Shadaloo, I love your MK3 fic. When are you going to continue it?