Actually, the idea of 'just war' vs. 'unjust war' were first developed by the non-religious (non-christian, anyway) rhetorician Cicero in his Republic.
Cicero actually split types of war into four categories: that is just, unjust, civil and 'more than civil' (foreign). Just war is that which is fought after the enemy was warned concerning the unjust loss of land or for the sake of fending off agressors (that have unjustly provoked the state). Unjust war is that which is begun from wrath rather than lawful reason. "Unjust wars are those begun without a reason. For there is no just reason for war outside of just vengeance or self defense." In more concrete terms, Cicero asserted that "no war is to be considered just unless it was openly announced and declared, unless reparation has first been demanded." (Republic 3,35) Thus, it is obvious that Augustine and Aquinas are quite indebted to Cicero for their ideas.
A very interesting discussion regarding this idea debates whether or not the Crusades were 'just wars.' In the jubilee year 2000, Pope John Paul II formally apologized for the Crusades (along with several other mistakes of the Holy Mother Church), implying that they were not. And that, I believe, is also the general concensus of today's Catholics and certainly non-Catholics. However, this is false.
Given, the Crusades were a human rights nightmare (as well as an utter military failure), and the Church has every reason to apologize for instigating them.* However, according to St. Aquinas and St. Augustine's definitions, they were perfectly legitimate! According to the Church's official line at the time, the Crusades were meant to protect Christian lands and peoples from imminent destruction by the infidel hordes. This translates to a direct attack against God. The Crusades, then, were the holiest type of war that could have been fought: in defense of God!
Before you scoff, remember also that Augustine and Aquinas' ideas were no Geneva Convention. They spent very little consideration on how a war could be carried out, only why one could be carried out (given, Aquinas dwells on the morality of a few military starategies, such as ambush). I'm sure they would not have approved of the torture, looting, raping, murdering, and dispossession of thousands of people that occurred during the Crusades, and certainly not the sack of a Christian city that occurred in the Sixth Crusade, but these issues were not raised in conjunction with the just war doctrine, at least, not at the time.
*Keep in mind, I am a pacifist (albeit a cynical one), and I don't think there should be any just reason to fight a war. And not being especially churchy I am especially against the idea of any kind crusade or jihad.