The Second Amendment. A well regulated Militia, being necessary to the security of a free State, the right of the people to keep and bear Arms, shall not be infringed.

See above.

The Third Amendment. No Soldier shall, in time of peace be quartered in any house, without the consent of the Owner, nor in time of war, but in a manner to be prescribed by law.

I could not find any links between America's prosecution of the war on terror and the Third Amendment, but I did find an excellent law review article suggesting that the individual rights contained in the Third Amendment may have been violated by National Guard troops sent to Louisiana and neighboring states in the immediate aftermath of Hurricane Katrina.

The Fourth Amendment.The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.

The war on terror has had the most effect of all upon Fourth Amendment rights. Bush Administration officials concluded early on in the process that the Fourth Amendment should be applied differently during a time of war. This is why you may be searched without probable cause at airports and why government agents may be listening in to your telephone conversations even if they have no judge's warrant to do so. It is why so many men after 9/11 were picked up on "material witness" warrants and held for months without trial. Read this for a sense of the debate on Capitol Hill on this in 2003.

The Fifth Amendment. No person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a Grand Jury, except in cases arising in the land or naval forces, or in the Militia, when in actual service in time of War or public danger; nor shall any person be subject for the same offence to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation.

This is the Amendment that was neutered so broadly after 9/11 that federal lawyers and, initially, the courts, willingly detained U.S. citizens (like Jose Padilla and Yaser Esam Hamdi) without giving the men access to their lawyers. It is this amendment which mainly impacts the still-addled military tribunals at Guantanamo Bay, Cuba. Today, meanwhile, overseas drone strikes, which have targeted even U.S. citizens, represent the most invasive and permanent intrusions upon due process rights.

The Sixth Amendment. In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the Assistance of Counsel for his defence.