Neo is a computer program... Multiple elements of proof: 1) After stopping the sentinals, he was stuck in the Train Station (how you get things into & out of the Matrix);
2) He could be in a human body the same way thet Smith was;
3) This explains his subsequent powers in the world of Zion, he can manipulate the programs through the machine world like a networked computer program could;
4) he realized that he was a program at the end of Revolutions, this is why he was willing to sacrifice himself WITHOUT telling the true story of the multiple reiterations of the Matrix to anyone @ Zion.;
5) The Architect says that only a fraction of a fraction of a percent of humans are like him (we only know about 8-10 out of billions of human beings);
6) Neo can see code just like other programs in the Matrix can;
7) The Oracle as much as told Neo he was a program by only comparing his abilities to choose to other programs, Neo does not figure this out until later, it is debatable whether Trinity knows or not;
8) He is completely emotionless, and EVERYONE involved in the movie said Reeves would be EXCELLENT in this part that requires showing few if any emotions!;
9) Incidental irony by him being a PROGRAMMER/HACKER in the Matrix world.
10) Smith had a special hatred for Neo because he could NEVER understand a rebel program (hence his questioning Neo's motives ("Surely you must see by now. You can't win against me...; why keep fighting, etc.");
11) Neo is Smith's opposite, the opposite of an Agent program working against humans is The One program working for humans
I think I've made my point.