Trivia: It's been said that Neo being an anagram for "one". I think it's more important to realise that Neo means "new". His real name is Thomas Anderson. He is called Thomas at the beginning of the movie, when he doubts the truth -- that the world as he knows it is not real. Thomas is the "doubting" disciple in the Bible. Moreover, Anderson means "son of man". Hence, Neo Anderson is the New Son of Man. The biblical references go on and on... Trinity, Nebucadnezzar (the name of the ship -- in fact, the name plate on the ship makes reference to a verse in Mark chapter 3), Zion... So not only is Neo "the One", he has gone from being the doubter to the new son of man.
Agent Smith: I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species, and I realised that you're not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment; but you humans do not. You move to an area and you multiply, and multiply, until every natural resource is consumed and the only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer on this planet, you are a plague, and we...are the cure. (01:02:20)
Agent Smith: Can you hear me, Morpheus? I'm going to be honest with you. I... Hate this place, this zoo, this prison, this reality, whatever you want to call it. I can't stand it any longer. It's the smell, if there is such a thing. I feel saturated by it. I can taste your stink. And every time I do I feel I have somehow been infected by it. It's repulsive, isn't it? I must get out of here. I must get free and in this mind is the key, my key. Once Zion is destroyed there is no need for me to be here, don't you understand? I need the codes. I have to get inside Zion, and you have to tell me how. You're going to tell me, or you're going to die.