The first concept that pops into my mind with this question is the following: "Is enhanced interrogation torture?" I think that this becomes one of the most pressing and powerful questions brought out by the UN Protocol. It is a part of the American political discourse right now. This past week, the Republican candidates stood on stage in front of the American public and pretty much agreed that "enhanced interrogation techniques" such as waterboarding is not torture. Ron Paul was the lone voice of dissent. In America, the current climate has associated "enhanced interrogation" with acceptable means that somehow demonstrates a commitment to finding and discovering vital information. I think that it would be really interesting to compare the Bush Administration's notion of "enhanced interrogation" with how the United Nations and the international community has defined and agreed to the idea of what defines "cruel" or "inhuman" or "degrading" methods of treatment of human beings. Prior to 2001, I think that most Americans would have allied themselves with the United Nations standards outlined in the document quite easily. Yet, the last decade has seen a noticeable shift and it might be interesting to bring this protocol back in light of this change in advocacy. It is highly contemporary and something that will end up playing a major role in both how the nation conducts itself in the future and how other nations will perceive it in the future.
When you say "applied to" I assume you are not asking about how it could be enforced. Instead, I assume that you are asking how the convention applies to or is relevant to a given conflict.
One of the provisions of the convention is a definition of torture. One part of the definition is that torture includes any action
...by which severe pain or suffering, whether physical or mental, is intentionally inflicted on a person for such purposes as ... intimidating or coercing him or a third person...
One way in which this aspect of the convention is violated is the use of rape as a weapon of war. As the economist.com link below shows us, rape has come to be used systematically to coerce and intimidate opponents in the various conflicts in African countries today. This is surely a case in which the convention applies, even though it would be extremely difficult to try to enforce it.