Michael Walzer's Just and Unjust Wars: A Moral Argument with Historical Illustrations is by now a classic in the theory of just and unjust war. There is a lot in the book that can be agreed with and disagreed with, and I will not trouble here to go in to a lengthy discussion of the book right now, the book has been reviewed over and over again already. The book covers a lot of the things you would want to address when talking about wars and morality. There is ample discussion of when a war is just, and what are just and unjust methods of fighting a war. There is a discussion of nuclear deterrence, emergencies, and terrorism, among many other things.
There is only one thing that would hold me back from recommending this as a good place to start if you want a presentation of a relatively modern academic discussion (from 1977) of what the issues in Just War Theory are - the presentation is a bit hard to follow. The historical illustrations are really helpful, but the discussions are often a bit prolix, and somewhat dense. The book could use to loose a few pages.
It really is a well thought out book, and despite the massive amount of literature that has already built up around it, both favorable and critical, it deserves to be widely read - especially these days when there is so much talk about justice and war, and so little corresponding thought.