Theory on How Neo Stopped the Sentinals/Smith-Bane
I just thought of this.
First, we know that in the "real world" the people can jack into a computer and download information like Kung Fu and how to fly a helicopter. This can also be done while in the Matrix.
Second, we know that whatever a person learns in the Matrix, he/she takes back to the real world. For instance, when people jack in and go have their talk with the Oracle they remember what she told them. Likewise, if they jacked into the Matrix, and went to school in the Matrix to be a doctor, they would remember the training and such after they unplugged.
Next, scientist say we only use 10% of our brain, and that if we used more, who knows what we could do.
So, my theory is that either the Oracle's candy or being close to the source or something else showed Neo how to open up the other 90% of his brain (or some portion). This gives him some type of telekentic or other powers that he can use against the Sentinals when he is outside of the Matrix.
This could also explain how Smith is able to live outside the Matrix. It is more like Bane's mind is lost. The cells "remember" what happened after Smith took him over. They are now functioning as a Smith.