@segdeha: Violating the 4th Amendment could be a criminal or civil matter. But as the article you link to describes, it is not clear whether the electronic surveillance methods currently used by the Bush Administration violate the 4th as the U.S. Supreme Court has specifically not addressed the issue when the government has a foreign relations/national security interest. Further, it is really a misnomer to call this a "Bush program." Actually, the methods currently used are updated forms of programs that go all the way back to WWII, thus you can't really attribute them to either party or an administration.
Those attacking the Bush Administration for these programs are mistaken or engage in selective memory. The Clinton administration expanded previously existing programs during Mr. Clinton's term from a focus on communications with foreign nationals regarding national security to a much more intrusive and broader program that included virtually every cell phone and e-mail communication in the U.S. The search protocols of the Clinton program, called ECHELON, were expanded from national security concerns such as communist, drug control and terrorist targets under Reagan and Bush Sr. to include party affiliation, unpopular political positions and alliances and even no governmental justification whatsoever. The Bush administration has actually limited and restricted the intrusive scope of surveillance previously used by the Clinton administration. As the Clinton Administration admitted in June 1996, it unlawfully obtaining over 400 restricted FBI files on U.S. citizens for political reasons, I wonder what they may have used ECHELON information for. In fact, Clinton appointees still in place in the NSA were very upset when shortly after the Bush administration took office then National Security Adviser Condoleeza Rice inadvertently confirmed the existence of ECHELON in a press conference. Thus, the Clinton administration engaged in far more indiscriminate and intrusive surveillance for less justifiable cause.
I believe an argument could be made that surveillance of phone and e-mail communications, when there are national security concerns, is not violative of the 4th Amendment. I'm not going to be able to give case names here, but there are two U.S. Supreme Court cases which determined there is a reduced expectation in privacy in "broadcasted" information. In these cases, there was no national security issue, these were domestic criminal cases. In the first, police used infrared detectors to determine unusual heat emissions from a residence consistent with the use of "grow lamps," obtained a warrant, and discovered a substantial indoor marijuana farm. The defendant argued the "viewing" of the heat signature of his residence was a 4th Amendment intrusion. The Court held as the infrared emissions were "broadcast" from the residence, this was not the same as planting a camera, and no 4th Amendment intrusion. In the second case, police could not obtain a warrant for a pay phone used by a suspect. Instead, an undercover officer stood next to the phone booth and recorded the phone conversation from outside the booth. The Court held as this sound was "broadcast" from the booth, it was not the same as recording with a bug located in the booth, and not a 4th Amendment violation. In the same manner, when you transmit a cell phone broadcast, or transmit an e-mail, you INTEND for it to be broadcast and received. It is arguable that the fact an unintended person, as in the two cases above, received the transmission and used it for a purpose not intended by the transmitter, is not itself a violation of the 4th Amendment. There is no clear authority the electronic surveillance currently used is a violation of the 4th Amendment, and I would imagine the Supreme Court for many reasons will avoid hearing this issue until it is inescapably placed before them.
As to the 1996 war crimes act, the article you link to clearly gives the reasons why amendments to the act are sought by the Bush Administration. The act simply refers back to and criminalizes violations of the Geneva Conventions. The amendments seek to replace the broad and vague language of the Conventions with a list of specifically proscribed acts. The reason is quite simple. Military and intelligence personnel cannot be expected to act without specific instructions, or they will be prone to be placed in jeopardy of prosecution by hindsight second guessing evaluation of their acts. The Geneva Convention uses broad language like "outrages upon personal dignity." This could mean a lot of things. The proposed amendments would give a list of specific acts that could not be done. Personnel would not have to guess whether making a detainee stay awake for days, stand in place for hours, wear soiled clothes because they have not been permitted to use a toilet, or threatening them with no dessert for a week would be an "outrage upon personal dignity." While you may feel the Bush Administration's list omits a number of acts that should be prohibited, certainly clarity is a helpful goal. If by avoiding prosecution you mean knowing what they can and can't do, ahead of time, then that is what they are doing.
There is also a valid argument the Geneva Conventions, written over 50 years ago, fail to include in their scope the current situation. The Geneva Conventions target the actions of the military forces and civilian populations of sovereign nations, and do not include multinational terrorist organizations that engage in guerilla and terrorist operations. In fact, the Geneva Conventions specifically exclude these organizations. They also do not include the current problem where the citizens of neutral nations are fighting in a war zone. Again, the Convention specifically excludes, say, Saudis captured in Iraq, as the citizens of neutral countries that have normal diplomatic relations are not covered as it is the responsibility of their nation to secure their rights. If the Saudi government chooses to do nothing, as they have, the country holding the detainee is not legally (as opposed to morally) required to apply the Geneva Convention. See: http://www.asil.org/insights/2004/10/insight041027.htm Also see: http://www.jewishvirtuallibrary.org/jsource/History/Human_Rights/geneva1.html
@chris6137: Invoking executive privilege is nothing new and has been done by administrations of both parties. Put simply, it is neither desirable nor effective for every act of a government to be subject to public scrutiny. For instance, exposing military and intelligence operations can result in the unnecessary loss of life. While you may disagree with the breadth of the Bush Administration's invocation of executive privilege, and it may turn out upon judicial review to have been excessive, at least it has been invoked to preserve at least arguably justified government concerns, and not, as in the Clinton Administration, to cover up oral sex. Further, at least the Bush Administration is bothering to acknowledge the existence of the information and claim executive privilege, rather than doing what the Clinton Administration usually did, either ignore court orders (they still haven't complied with a number of orders), deny the information exists (then it turns up, say, in Ms. Clinton's living quarters) or destroy the information (a large number of e-mails and printed records ordered to be turned over by various courts were intentionally destroyed by the Clinton Administration when they left office). And let's not forget stealing the documents from the National Archives when Congressional hearings become troublesome.