[QUOTE=glee]
As usual, I like your logical approach. 
However I do disagree on one point.
I oppose the death penalty, but accept wars in genuine self-defence.
I also support the right of an attacked person to use appropriate force (lethal if the threat is lethal).
The difference is that society has control over a convicted murderer and can use other means of punishment / rehabilitation (plus not all convictions stand the test of time).
[/QUOTE]
In a way, I think you are reinforcing John Mace’s point (correct me if I’m off-base, John Mace). The OP is assuming that all of the examples given are coming from the same moral place, and should all have the same rationale or justification. Pro-life philosophy/theology is a little more complicated than “all killing is wrong.” It’s a nice idea in theory, but in practice in the real world, it’s not nearly that simple. Not only are all the ideas not analagous, but as you are showing by your post, reasonable people can disagree about what is or is not morally justified. A few considerations that may be taken into account might be the following:
(Please note that I am not proposing that we debate whether or not fetuses are babies, or whether or not the war in Iraq is justified, or whether or not civilians are being deliberately targeted in the war, or whether the death penalty is applied fairly, etc. etc. etc. There is no point in challenging any of these premises in this thread. You may or may not agree with any of them. The question was how are these perceived moral contradictions resolved. John Mace made the point already that you have to understand that various premises may be at work, and I am attempting to explain a few of those premises.)
Innocence: In capital punishment, the innocent are not being killed. Completely different to punish someone for taking a life, vs. killing innocents in war and/or for medical research.
Deliberateness: In a war, innocents may or may not be killed, and more importantly need not necessarily be killed in order to be successful. In additon, war is waged directly against a specific group of people who presumably mean harm to others. In fetal stem cell research, innocent lives who clearly do not intend harm to others are specifically and deliberately created and destroyed.
Purpose & Outcome: In a war, saving an entire nation (or, frighteningly enough in this age, the entire world) may be at stake. In fetal stem cell research, saving a finite and relatively small number of people is the desired outcome. While this is a noble purpose to be sure, it is not an analagous situation.
One last note: although some of the posts here seem to assume that all people who oppose fetal stem cell research are in favor of the Iraqi war, this is far from the truth. The previous pope came out against this war. Although the Catholic Church does not condemn justified wars, apparently JPII did not feel that this particular war IS justified.