1. Jewish ethics clearly distinguish between the different categories of war. An obligatory war (milchemet mitzvah) requires a different mode of ethical conduct than all other types of war. Particularly when discussing the obligation in the time of Joshua to conquer the land of Israel for the first time and the generic biblical obligation to destroy Amalek, Jewish law mandates a different set of ethical norms for these historical obligations.
Thus Maimonides states:
It is a positive commandment to vanquish the seven nations [that used to occupy Israel] since it says “you shall vanquish them.” Anyone who has one of the members of that nation subservient to him and does not kill him violates the negative commandment, since it says “no life shall survive [from the seven nations].” Their identity has since disappeared.
(Note: If we no longer have a Divine commandment to vanquish any remaining people or nation, how do we justify killing them?)
2. The Talmud additionally recounts that there are three ritual requirements for an Authorized war (milchemet rishut) to commence. The first is the consent of the Sanhedrin (Parliament); see Sanhedrin 29b. The second is the presence of a king or ruler; see Sanhedrin 20a. The third is consultation with the urim vetumim, a mystical ornament worn by the High Priest (not in existence for more than 3000 years); see Sanhedrin 16b. (For an explanation of what this garment precisely is, see Maimonides, K'lei Mikdash, 8:1-6.)
A number of commentators significantly limit each of these three Talmudic requirements. Maimonides does not list the requirement of urim vetumim at all in his code. He does, however, state elsewhere (see Book of Commandments, chapter 14) that the urim vetumim are needed. So too, Aruch HaShulchan HeAtid, Melachim 74:7 states that the Urim are not needed and this is agreed to by R. Zevin, L`Or Hahalacha, p. 12. Nachmanides states (see Addendum to Maimonides Book of Commandments, positive commandment 4) that a king is not actually needed. Rather war may be undertaken by “a king, judge, or whoever exercises jurisdiction over the people.” The Meiri argues that approval of the Sanhedrin is only needed if a significant minority of the nation does not approve of the war. However, he states that no approval is needed for popularly supported wars; see Sanhedrin 16a.
3. The question of who is “innocent” in the context of war is difficult to quantify precisely. One can be a pursuer in situations where the law does not label one a “murderer” in Jewish law; thus a minor (Sanhedren 74b), and according to most authorities, an unintentional murderer both may be killed to prevent the loss of life of another. So too, it would appear reasonable to derive from Maimonides' rule that one who directs the murder even though he does not directly participate in it is a murderer, and may be killed. So too, it appears that one who assists in the murder, even if they are not actually participating in it directly is not “innocent”; see comments of Maharal M'Prague on Genesis 32. From this Maharal one could derive that any who encourage this activity fall within the rubric of one who is a combatant.
(Note: It's not hard to deduce that the behind-the scenes “masterminds” who encourage others to commit suicide bombings are indeed murderers themselves. It's much harder to determine whether the civilians on both sides of the Palestinian-Israeli conflict are implicated for their complicity in the violence.)
All emphases and notes are added. The full article can be viewed at http://www.jlaw.com/Articles/war1.html