Probably the central argument in the Apology is that one should never betray one's own philosophy for any reason, even if the reason is death.  Moreover, death should never be a deterrent to a man (especially a philosopher) because no man has true knowledge of death, and "surely it is the most blameworthy ignorance to believe that one knows what one does not know".  Plato and Socrates firmly believed that we have no cause to fear death, and as stated in a previous quote, for the philosopher death was probably a more desirable state to be in than life because one could reason and contemplate the Forms without the hindrance of perception and the body.  Philosophers were people who pursued wisdom, and according to Plato, the best way to do this was from the mind alone without the body.  He believed that the state of one's soul was of the utmost importance because one's place in the afterlife and next life was determined by the state of their soul.  Arguments on the soul are further considered in the Phaedo. 

Another important aspect of this work is the respect for the laws that Socrates shows throughout his trial.  He has a dedication that Plato thought necessary to exploit, probably because the state of Athens was struggling politically when this was written.  There were crooked government officials and a juggling of government types going on within the city.  Socrates was a good citizen who respected the what was good and right, and a man who held the laws in high regard because he believed in them.

And a final major theme of the Apology is the dedication of Socrates to his philosophy, despite the opposition of the majority.  It could be questioned if Socrates didn't bring his persecution on himself, with the way that he questioned everything and everyone.  It sometimes seems understandable that his fellow citizens would become intolerable of such a man, but never once does he apologize for his actions.  He cares more for being a good and upright man than being popular with the people.  He cares more for the pursuit of knowledge than the pursuit of success and wealth.  And he cares more for the souls of himself and others, and when seen in that light, the failure of justice was on the part of those who did not accept him, not himself.