Idealogian

Do the same rules apply against Amalek? If not, how does one discern who today is Amalek?

Nevermind Amalek, in in the Perek that is cited, we are told that even in a permissible war we must kill every male -- unless they offer peace and we take them as slaves.
(Note that the saving of Women and Children is NOT for humanitarian reasons, rather to exclude the males: ONLY Women and Children may be enslaved!)
Also, look at the Talmudic description of the last days of Bayit Sheni and you may reconsider the sensitivity of seig warfare. As for Baal Tashchit, it seems difficult to say that it is to be more sensitive to the enemy, rather a more environmental concern.
Most of Sefer Yehoshua is pretty gruesome and it is clear taht when Bnei Israel need a victory they are told to achieve it at high costs. None of these prohibitions apply during a Mitzva war.

Dad -
I'm not sure whether/how these halachot apply to wars with Amalek, though perhaps I'll try to look into that. (Danny seems to be saying that they wouldn't, and I see no reason not to trust him on that.)

In any case, "allah Sancheiriv melech Ashur uvilbeil et kol ha'umot" - we no longer know who originated as part of what nation. Rav Soleveitchiks' stance that the Nazis/Germans were considered Amalek (i.e., Amalek is defined by ideology and not just genealogy) seems to be somewhat of a chiddush and, to my knowledge, was applied practically only in that he prohibited accepting reparations from Germany (something that is clearly not universally accepted). I highly doubt that he would have advocated killing every man, woman and child living in Germany in the '30s-'40s. Especially since the notion of nationality is significantly weaker today than it was millennia ago - one can live in Germany without being a German. And I think that one can even be a citizen of Germany without really being part of the German nation. (I realize that I'm being imprecise here in my distinction between "German" and "Nazi," but that's the same thing one would be doing to equate "Palestinian" with "Hamas terrorist," or "Iraqi" with "Wahhabist.")

Danny -
I never said anything about saving people for humanitarian reasons or being sensitive to the enemy. It's impossible to shoot your enemy gently. And even were it possible, it wouldn't necessarily be advisable. Other enemies might see it and say, "Hey, that doesn't look so bad. Just a mild discomfort really." But that doesn't mean that you should smile as you shoot him.

"Lo nitnu hamitzvot ella l'tzareif bahen et hab'riyot" - mitzvot are (at the very least) intended to effect a certain change within our own nature. These particular mitzvot seem to me (though you could very easily argue this point) to aim towards a rejection of a "win at (not just high but) all costs" mentality, an aversion to wanton destruction, and a preference for peace over war and unnecessary loss of human life. Where we draw the line of high costs, what's defined as "wanton," how strong that preference is and what's considered "necessary" - well, fortunately, I'm not currently a warrior and therefore that's not a practical judgment I need to make. But it's still a concern I feel I should be pondering, all the more so those who are involved in such decisions. The fact that we don't know where to draw the line doesn't mean that we needn't try to determine where it should be, and it certainly doesn't mean that there is no line.

How would you reconcile your position with the following idea: כל הרחמן על האכזרים םוף נעשה אכזר על הרחמנים

Devorah -
Cool! Hebrew! Didn't know one could do that on my blog. How'd you do it?

Regardless, it's a good question, and something I meant to address in my previous comment but forgot to. I'll start by translating for those who may not understand or have Hebrew fonts. "One who is merciful to those who are cruel, in the end will become cruel to those who are merciful." I'll also provide the context of this quote (though I can't find a precise reference anywhere online to link to): Chazal are describing King Shaul, who had mercy on Aggag, king of Amalek and chose to let him live; Shaul later wiped out the entire city of Nov, some of whose inhabitants had helped David in his escape from Shaul.

So Chazal are telling us not to be merciful to those who are cruel. But figuring out what that entails requires a definition of the terms:

1. What do you consider "merciful?"

Suppose I capture a dangerous enemy in war (let's even suppose that he's a really mean guy), and then find myself pondering whether I should flay him alive and force him to watch as I feed his skin to my dog, not as a deterrent to other enemies, but simply because I'm bored and my dog is hungry. Personally, I think I would probably choose not to do this. But would I blame someone who chose to do so? Most certainly. Why? Isn't that asking him to be merciful to one who is cruel? Well, some might call it merciful; some might call it human. Perhaps it's asking him to be sensitive to the innate tzelem Elokim present in every human being and to avoid unnecessarily degrading that aspect (the "ma'asei yadai tov'im bayam" factor, if you will).

Now, let's tone it down a bit. Suppose I capture an enemy in war and then find myself pondering whether I should burn him with cigarettes, put a bag over his head and take pictures of him naked while I point and laugh, or put him on a leash. Would I do those things? Maybe, if I thought they were useful interrogation techniques (though I'm not sure how much I buy that). Would I blame someone who chose to do them? Not necessarily. But I would blame someone who chose to do them without giving any thought to his or her actions, and did so simply because, well, why not? In other words, I expect that even warriors should be sensitive to considerations of basic human dignity, even if those considerations don't always end up dictating a course of action.

2. Whom do you consider "cruel?"

Certainly, bin Laden is evil and cruel, as are any suicide bombers, active terrorists, etc. I don't advocate going easy on them. But what about Palestinian women and children (and men as well, I suppose) who are not involved in terrorist activities and don't even support them? I am in favor of the security barrier as a necessary measure, but I also believe that it should be built with sensitivity to the hardship it is causing those who are innocent of any wrongdoing. If there's nothing that can be done to improve that situation, OK; we do need to put our own lives first. But that doesn't mean we don't need to ask the question and be sensitive to the consideration.

(I would also question whether even Iraqi soldiers legitimately fighting to defend their country from what they reasonably perceive to be invaders fit the definition of "cruel" - certainly not in the same way that Aggag/Amalek was.)

I've highlighted the two points that I feel come into play in the two "l'ma'aseh" examples I linked to at the end of my post. I originally chose not to discuss practical examples because that wasn't my point. I'm not trying to say, "Here's what should be done in this situation," because I don't claim to know precisely what we should do in any given situation. I'm simply saying, "Here's what should be considered in any situation."

Hmm…I couldn’t find the exact quote online either, but I did find this:

דמילתא (שמואל א טו) וירב בנחל אמר ר' מני על עסקי נחל בשעה שאמר לו הקב"ה לשאול (שמואל א טו) לך והכית את עמלק אמר ומה נפש אחת אמרה תורה הבא עגלה ערופה כל הנפשות הללו על אחת כמה וכמה ואם אדם חטא בהמה מה חטאה ואם גדולים חטאו קטנים מה חטאו יצאה בת קול ואמרה לו (קוהלת ז) אל תהי צדיק הרבה ובשעה שאמר לו שאול לדואג (שמואל א כב) סוב אתה ופגע בכהנים יצאה בת קול ואמרה לו (קוהלת ז) אל תרשע הרבה

BTW, nice answer. Thanks for clarifying.

Just about the security fence.... It was not Israel's first choice. First choice was containment, keep all the Palestinians in their towns during times of hightened security alerts. In case you don't remember, because of continual threats, the temporary measure became more and more permanent (the year we were in Gush, during the height of the Oslo process, the PA towns were under seger over 65% of the year!). Soon, the closures became unbearable and Israel was accused of collective punishment. Then we tried open negotiations at Camp David, which were either very concessionary or simply a stalling tactic, depending on who you believe. Next we tried targeted killings, specifically to AVOID the claim of COLLECTIVE punishment. This was looked down upon by the international community.
The fence is in a way a very targeted measure because it focuses on stopping Arabs that want to reach Israeli population centers illegaly. While it does "punish" those innocents who happen to live near the green line, it also relieves some Arabs inside the green line by eliminating the need for some check points. The farther in the fence goes the easier free movement BEHIND the fence becomes, and only a small percentage on the periphery are effected. However, these facts are conspicuously left out from the complaints filed against the fence by those who actually are effected.