I wanted to know how Neo knew it was Morpheus on the phone during the scene at his job (the scene with the cubicles).
Neo knows other hackers (he knows who Trinity was before she was freed from The Matrix) so I assumed this is how he knows a Morpheus. However, he knows Morpheus by voice which is not something people do often over the computer (especially when they are hackers).
I also wanted to know how Neo knows about The Matrix. During the scene where he first meets Trinity she says that she knows what he is looking for and whispers "The Matrix".
Both these points make me feel like Neo had some things to do with The Matrix before the events of the movie. I know that he has a hunch that something isn't right but these things make it appear asif he was already doing stuff against the matrix from within before being freed.