Felipe Sixto, was appointed by President George W. Bush to be his Special Assistant for Intergovernmental Affairs as well as Duty Director of the Office of Public Liaison. He resigned a few weeks later on March 20, 2008 because of his alleged misuse of grant money from the U.S. Agency for International Development when he worked for the Center for a Free Cuba. He was sentenced to 30 months in prison for stealing almost $600,000 for his own use.
Timothy Goeglein Special Assistant to President Bush resigned when it was discovered that more than 20 of his columns had been plagiarized from an Indiana newspaper. (2008)
Scott Block was appointed by President George W. Bush to head the Office of Special Counsel. On April 27, 2010 Bloch pleaded guilty to criminal contempt of Congress for "willfully and unlawfully withholding pertinent information from a House committee investigating his decision to have several government computers wiped ...." On February 2, Magistrate Judge Deborah A. Robinson ruled that Bloch faces a mandatory sentence of at least one month in prison.
Lewis Libby Chief of Staff to Vice President Dick Cheney (R). 'Scooter' was convicted of perjury and obstruction of justice in the Plame Affair on March 6, 2007. He was sentenced to 30 months in prison and fined $250,000. The sentence was commuted by George W. Bush (R) on July 1, 2007. The felony remains on Libby's record though the jail time and fine were commuted.
Alphonso Jackson The Secretary of Housing and Urban Development resigned while under investigation by the Justice Department for alleged cronyism and favoritism 
Karl Rove Senior Adviser to President George W. Bush was investigated by the Office of Special Counsel for "improper political influence over government decision-making", as well as for his involvement in several other scandals such as Lawyergate, Bush White House e-mail controversy and Plame affair. He resigned in April 2007. (See Karl Rove in the George W. Bush administration)
Richard J. Griffin Assistant Secretary of State for Diplomatic Security appointed by George W. Bush who made key decisions regarding the department's oversight of private security contractor Blackwater USA, resigned in November 2007, after a critical review by the House Oversight Committee found that his office had failed to adequately supervise private contractors during the Blackwater Baghdad shootings protecting U.S. diplomats in Iraq.
Howard Krongard, Republican contributor was appointed Inspector General of the US State Department by President George W. Bush in 2005. After he was accused by the House Oversight Committee of improperly interfering with investigations into private security contractor Blackwater USA, concerning the Blackwater Baghdad shootings. Krongard resigned in December 2007.
"Lawyergate" Or the Dismissal of U.S. attorneys controversy refers to President Bush firing, without explanation, eleven Republican federal prosecutors whom he himself had appointed. It is alleged they were fired for prosecuting Republicans and not prosecuting Democrats. When Congressional hearings were called, a number of senior Justice Department officials cited executive privilege and refused to testify under oath and instead resigned, including:
1.Michael A. Battle Director of Executive Office of US Attorneys in the Justice Department.
2.Bradley Schlozman Director of Executive Office of US Attorneys who replaced Battle
3.Michael Elston Chief of Staff to Deputy Attorney General Paul McNulty
4.Paul McNulty Deputy Attorney General to William Mercer
5.William W. Mercer Associate Attorney General to Alberto Gonzales
6.Kyle Sampson Chief of Staff to Attorney General Alberto Gonzales
7.Alberto Gonzales Attorney General of the United States
8.Monica Goodling Liaison between President Bush and the Justice Department
9.Joshua Bolten Deputy Chief of Staff to President Bush was found in Contempt of Congress
10.Sara M. Taylor Aide to Presidential Advisor Karl Rove
11.Karl Rove Advisor to President Bush
12.Harriet Miers Legal Counsel to President Bush, was found in Contempt of Congress
Bush White House e-mail controversy – During the Lawyergate investigation it was discovered that the Bush administration used Republican National Committee (RNC) web servers for millions of emails which were then destroyed, lost or deleted in possible violation of the Presidential Records Act and the Hatch Act. George W. Bush, Dick Cheney, Karl Rove, Andrew Card, Sara Taylor and Scott Jennings all used RNC webservers for the majority of their emails. Of 88 officials, no emails at all were discovered for 51 of them. As many as 5 million e-mails requested by Congressional investigators of other Bush administration scandals were therefore unavailable, lost, or deleted.
Lurita Alexis Doan Resigned as head of the General Services Administration. She was under scrutiny for conflict of interest and violations of the Hatch Act. Among other things she asked GSA employees how they could "help Republican candidates".
John Korsmo chairman of the Federal Housing Finance Board pled guilty to lying to congress and sentenced to 18 months of unsupervised probation and fined $5,000. (2005)
Philip Cooney Bush appointee to chair the Council on Environmental Quality was accused of editing government climate reports to emphasize doubts about global warming. Two days later, Cooney announced his resignation and later conceded his role in altering reports. Stating "My sole loyalty was to the President and advancing the policies of his administration," .
Jack Abramoff Scandal in which the prominent lobbyist with close ties to Republican administration officials and legislators offered bribes as part of his lobbying efforts. Abramoff was sentenced to 4 years in prison. See Legislative scandals.
1.David Safavian GSA (General Services Administration) Chief of Staff, found guilty of blocking justice and lying, and sentenced to 18 months
2.Roger Stillwell Staff in the Department of the Interior under President George W. Bush (R). Pleaded guilty and received two years suspended sentence. 
3.Susan B. Ralston Special Assistant to the President and Senior Advisor to Karl Rove, resigned October 6, 2006, after it became known that she accepted gifts and passed information to her former boss Jack Abramoff.
4.J. Steven Griles former Deputy to the Secretary of the Interior pleaded guilty to obstruction of justice and was sentenced to 10 months.
5.Italia Federici staff to the Secretary of Interior, and President of the Council of Republicans for Environmental Advocacy, pled guilty to tax evasion and obstruction of justice. She was sentenced to four years probation.
6.Jared Carpenter Vice-President of the Council of Republicans for Environmental Advocacy, was discovered during the Abramoff investigation and pled guilty to income tax evasion. He got 45 days, plus 4 years probation.
7.Mark Zachares staff in the Department of Labor, bribed by Abramoff, guilty of conspiracy to defraud.
8.Robert E. Coughlin Deputy Chief of Staff, Criminal Division of the Justice Department pleaded guilty to conflict of interest after accepting bribes from Jack Abramoff. (2008)
Kyle Foggo Executive director of the CIA was convicted of honest services fraud in the awarding of a government contract and sentenced to 37 months in federal prison at Pine Knot, Kentucky. On September 29, 2008, Foggo pleaded guilty to one count of the indictment, admitting that while he was the CIA executive director, he acted to steer a CIA contract to the firm of his lifelong friend, Brent R. Wilkes.
Julie MacDonald Deputy Assistant Secretary of the Department of the Interior, resigned May 1, 2007, after giving government documents to developers (2007)
Claude Allen Appointed as an advisor by President George W. Bush (R) on Domestic Policy, Allen was arrested for a series of felony thefts in retail stores. He was convicted on one count and resigned soon after.
Lester Crawford Commissioner of the Food and Drug Administration, resigned after 2 months. Pled guilty to conflict of interest and received 3 years suspended sentence and fined $90,000 (2006)
2003 Invasion of Iraq depended on intelligence that Saddam Hussein was developing "weapons of mass destruction" (WMDs) meaning nuclear, chemical and/or biological weapons for offensive use. As revealed by The (British) Downing Street memo "Bush wanted to remove Saddam, through military action, justified by the conjunction of terrorism and WMD. But the intelligence and the facts were being fixed around the policy" The press called this the 'smoking gun."(2005)
Yellowcake forgery: Just before the 2003 invasion of Iraq, the Bush administration presented evidence to the UN that Iraq was seeking material (yellowcake uranium) in Africa for making nuclear weapons. Though presented as true, it was later found to be not only dubious, but outright false.
Coalition Provisional Authority Cash Payment Scandal: On June 20, 2005, the staff of the Committee on Government Reform prepared a report for Congressman Henry Waxman. It was revealed that $12 billion in cash had been delivered to Iraq by C-130 planes, on shrinkwrapped pallets of US $100 bills. The United States House Committee on Oversight and Government Reform, concluded that "Many of the funds appear to have been lost to corruption and waste.... Some of the funds could have enriched both criminals and insurgents...." Henry Waxman, commented, "Who in their right mind would send 363 tons of cash into a war zone?" A single flight to Iraq on December 12, 2003, which contained $1.5 billion in cash is said to be the largest single Federal Reserve payout in US history according to Henry Waxman.
Bush administration payment of columnists with federal funds to say nice things about Republican policies. Illegal payments were made to journalists Armstrong Williams, Maggie Gallagher and Michael McManus (2004–2005)
Bernard Kerik nomination in 2004 as Secretary of Homeland Security was derailed by past employment of an illegal alien as a nanny, and other improprieties. On Nov 4, 2009, he pled guilty to two counts of tax fraud and five counts of lying to the federal government and was sentenced to four years in prison.
Plame affair (2004), in which CIA agent Valerie Plame's name was supposedly leaked by Richard Armitage, Deputy Secretary of State, to the press in retaliation for her husband's criticism of the reports used by George W. Bush to legitimize the Iraq war. Armitage admitted he was the leak but no wrongdoing was found.
Thomas A. Scully, administrator of the Centers for Medicare and Medicaid Services (CMS), withheld information from Congress about the projected cost of the Medicare Prescription Drug, Improvement, and Modernization Act, and allegedly threatened to fire Medicare's chief actuary, Richard Foster, if Foster provided the data to Congress. (2003) Scully resigned on December 16, 2003.
NSA warrantless surveillance – Shortly after the September 11 attacks in 2001, President George W. Bush (R) implemented a secret program by the National Security Agency to eavesdrop on domestic telephone calls by American citizens without warrants, thus by-passing the FISA court which must approve all such actions. (2002) In 2010, Federal Judge Vaughn Walker ruled this practice to be illegal.
Kenneth Lay, a member of the Republican National Committee, financial donor and ally of President George W. Bush (R) and once considered a possible Secretary of the Treasury. Lay was found guilty of 10 counts of securities fraud concerning his company Enron, but died before sentencing.
Janet Rehnquist (daughter of former Chief Justice William Rehnquist) appointed Inspector General of the Department of Health and Human Services by George W. Bush. In 2002, Governor Jeb Bush's (R-FL) Chief of Staff Kathleen Shanahan asked Rehnquist to delay auditing a $571 million federal overpayment to the State of Florida. Rehnquist ordered her staff to delay the investigation for five months until after the Florida elections. When Congress began an investigation into the matter, Rehnquist resigned in March 2003, saying she wanted to spend more time with her family.