This discussion may contain spoilers!
You have to keep an open mind as I know some of these are unlikely,
but improbable does not mean impossible.
In the end when Clementine says "I thought you were dead," I had a few thoughts on who it could be and who it could not be. After some time I put a lot of thought into this, and if you agree or disagree please discuss this like reasonable people. Or if you think it could be someone else, please discuss it as I would like to hear your input.
First the list of people who I don't think Clem is talking to in the ending.
(contains names I've seen in other threads and I'm just giving my thoughts on why I don't think it is them.)
Lilly - She was never killed in game nor mentioned to have died, so Clem would have no knowledge of death concerning her. Plus no real attachment to her.
Molly - Same as Lilly
Christa - If it was really Christa then Clem would've had a look of relief and would've said "You're alive!"(or something along that) with a smile on her face since she was in search of her. Instead, she had a discerning look with disbelief. No way it could be Christa.
Now onto the people I think it could be.
Kenny - Maybe he really did run off and Lee just assumed he was dead given the circumstances. Since we the audience didn't see an actual death scene, it gives the possibility that he survived the attack, but the rest of the group didn't see that.
Omid - We know he was shot in the chest early in the episode, but we had no real confirmation of his death. We didn't really see if Clem or Christa took the head shot so that Omid doesn't come back as a walker/lurker. For all we know he could have had a still heart from the shock; it has happened before in the real world. If they didn't take the shot then he could have still lived and was left behind. Just a theory I had.
Lee - Then there's the highly improbable off-chance if you didn't shoot Lee in the end of S1E5 and leave him behind that he survives and joins another group. This theory I doubt very much, but a theory nonetheless.