As a quick overview- Just War Theory lies in the middle of two extreme philosophical views on war - Militarism, which suggests that war should be an accepted part of our society and can be beneficial, and Pacifism, which states that war is always bad (morally unacceptable), and there is never an acceptable reason to engage in war. (Another interesting theory is "Realism" which suggests that countries are just going to do whatever is in their own best interest, regardless of philosophical issues of good and bad.)
Back to Just War Theory...
The first issue deals with whether or not a war can be just - under what conditions would it be ok to enter into war? Current Just War theory includes six main items in this topic.
1. Just Cause - You must be redressing a wrong or saving life.
2. Legitimate Authority - War can only be waged by governments or recognized political authorities (interpretation of this varies, particularly due to the issue of civil war.)
3. Right Intention - In addition to having a good reason (just cause) for going to war, you must have right intentions - you need to be correcting a wrong, not trying to gain territory or money, for example.
4. Probability of Success - You need to have a good chance of winning without using disproportionate measures. (i.e. If you're probably going to lose, or you need to bomb huge areas to win, since you can't fight conventionally, you shouldn't go to war.)
5. Last Resort - You have to have tried every other peaceful option unless the options are clearly not practical.
6. Proportionality - The benefits of waging the war have to outweigh the costs (evils or harms).
Waging a "Just War"
The other part of this theory is how to act "justly" when waging war. It has three main components.
1. Distinction - You have to make a distinction between civilians and combatants, and acts of war should be carried out towards combatants.
2. Proportionality - If civilian casualties are going to take place, they must be small in comparison to the military benefits of taking action.
3. Military Necessity - All actions should be taken only for military necessity, you cannot knowingly attack civilian/non-military targets.
I don't think I'll make any normative statements regarding this theory. Since I was just introduced to it, I'm still in the mode of just thinking it's interesting, rather than whether it's right or wrong (which seems to depend a lot on your view being theoretical vs. practical in my opinion).