Commerce, Justice, Science, and Related Agencies Appropriations Act, 2012

(Sec. 105) Sets forth determinations that must be made by the Under Secretary of Commerce for Oceans and Atmosphere in order for NOAA to enter a contract for development of a major program (an activity approved to proceed to implementation that has an estimated lifecycle cost of more than $250 million), including that the technical, cost and schedule risks of the program are clearly identified and that the program has demonstrated a high likelihood of accomplishing its intended goals. Requires the Under Secretary to annually submit a Major Program Annual Report that includes such required information for the satellite development program for which NOAA proposes to expend funds in the subsequent year.

(Sec. 110) Establishes in the Treasury a Fisheries Enforcement Asset Forfeiture Fund and a Sanctuaries Enforcement Asset Forfeiture Fund.

Title II: Department of Justice - Department of Justice Appropriations Act, 2012 - Makes appropriations for the Department of Justice (DOJ) for FY2012 for: (1) general administration, including for the National Drug Intelligence Center, the Federal Detention Trustee, and the Office of Inspector General; (2) the United States Parole Commission; (3) legal activities, including for reimbursement from the Vaccine Injury Compensation Trust Fund for processing cases under the National Childhood Vaccine Injury Act of 1986, the Offices of the United States Attorneys, the United States Trustee Program, the Foreign Claims Settlement Commission, the Community Relations Service, and the Assets Forfeiture Fund; (4) the United States Marshals Service; (5) the National Security Division; (6) interagency crime and drug enforcement; (7) the Federal Bureau of Investigation (FBI); (8) the Drug Enforcement Administration (DEA); (9) the Bureau of Alcohol, Tobacco, Firearms, and Explosives (ATF); (10) the federal prison system, including for Federal Prison Industries, Incorporated; (11) the Office on Violence Against Women for violence against women prevention and prosecution programs, including for establishment of a national clearinghouse to provide training and technical assistance on issues relating to sexual assault of American Indian and Alaska Native women; (12) Office of Justice Programs, including the Edward Byrne Memorial Justice Assistance Grant Program, the State Criminal Alien Assistance Program, the Northern and Southern Border Prosecutor Initiatives, the Capital Litigation Improvement Grant Program, an Edward Byrne Memorial criminal justice innovation program, the National Criminal History Improvement Program, and Paul Coverdell Forensic Sciences Improvement Grants; and (13) Community Oriented Policing Services.

(Sec. 202) Prohibits the use of funds to: (1) pay for an abortion, except where the life of the mother would be endangered if the fetus were carried to term, or in the case of rape; or (2) require any person to perform or facilitate an abortion.

(Sec. 217) Directs the Attorney General to report to the House and Senate Appropriations Committees a cost and schedule estimate for the final operating capability of the FBI's Sentinel program, which shall be submitted concurrently to DOJ's Office of Inspector General, which shall provide an assessment of it.

Title III: Science - Science Appropriations Act, 2012 - Makes appropriations for FY2012 for: (1) the Office of Science and Technology Policy; (2) the National Aeronautics and Space Administration (NASA) for science (including the James Webb Space Telescope), aeronautics, space technology, exploration, space operations, aerospace and aeronautical education research and development activities, for cross agency support, for construction and environmental compliance and restoration, and for the Office of Inspector General; and (3) the National Science Foundation (NSF), including for the Office of the National Science Board and the Office of Inspector General.

Title IV: Related Agencies - Makes appropriations for FY2012 for: (1) the Commission on Civil Rights, (2) the Equal Employment Opportunity Commission (EEOC), (3) the International Trade Commission, (4) the Legal Services Corporation, (5) the Marine Mammal Commission; (6) the Office of the United States Trade Representative, (7) the State Justice Institute, and (8) the Commission on Wartime Relocation and Internment of Latin Americans of Japanese Descent (established by this Act).

Title V: General Provisions - (Sec. 501) Sets forth requirements, restrictions, and limitations on the use of funds appropriated by this Act.

(Sec. 506) Prohibits the use of funds to implement, administer, or enforce any EEOC guidelines covering harassment based on religion when it is made known to the federal entity to which such funds are made available that such guidelines do not differ in any respect from the proposed guidelines published by the Commission on October 1, 1993.

(Sec. 507) Makes any person who mislabels a product sold in or shipped to the United States as "Made in America" ineligible to receive any contract or subcontract funded by this Act.

(Sec. 508) Requires the Department of Commerce, DOJ, NSF, and NASA to: (1) provide a quarterly accounting of the cumulative balances of any unobligated funds that were received by such agency during any previous fiscal year, and (2) submit spending plans within 30 days after this Act's enactment.

(Sec. 510) Prohibits the use of funds to promote the sale or export of tobacco or tobacco products or to seek the removal by any foreign country of restrictions on marketing of such products, except for restrictions which are not applied equally to all tobacco products of the same type.

(Sec. 511) Prohibits funding for the implementation of: (1) any user fee for background checks under the Brady Handgun Control Act of 1993; or (2) any background check system that does not require and result in the destruction of information submitted by an individual certified as eligible to possess or receive a firearm.

(Sec. 513) Prohibits the use of DOJ funds to discriminate against or denigrate the religious or moral beliefs of students who participate in DOJ programs, or of the parents or legal guardians of such students.

(Sec. 516) Declares that ATF firearms tracing studies are released without adequate disclaimers regarding the limitations of the data.

(Sec. 518) Prohibits the use of funds to: (1) issue patents on claims directed to or encompassing a human organism; (2) support or justify the use of torture by any official or contract employee of the U.S. government; (3) pay administrative expenses or to compensate any U.S. officer or employee of the United States in connection with requiring licenses for exporting certain firearms to Canada with a total value not exceeding $500 wholesale in any transaction or denying certain import applications regarding curios or relics, firearms, parts, or ammunition; (4) include in any new bilateral or multilateral trade agreement certain language of the United States-Singapore Free Trade Agreement, the United States-Australia Free Trade Agreement, or the United States-Morocco Free Trade Agreement; or (5) authorize or issue a national security letter in contravention of specified statutes authorizing the FBI to issue national security letters.

(Sec. 526) Requires departments, agencies, and commissions funded under this Act to establish and maintain on their Internet websites direct links to their Offices of Inspector General, and a mechanism for anonymously reporting waste, fraud, and abuse.

(Sec. 527) Prohibits the use of funds under this Act: (1) to award a contract or grant in an amount greater than $5 million unless the recipient certifies that it has filed all federal tax returns required during the preceding three years, has not been convicted of a criminal offense under the Internal Revenue Code, and has not been notified of any unpaid federal tax assessment for which the liability remains unsatisfied; or (2) in a manner that is inconsistent with the principal negotiating objective of the United States with respect to trade remedy laws to preserve the ability of the United States to enforce vigorously its trade laws, to avoid agreements that lessen the effectiveness of domestic and international disciplines on unfair trade or safeguard provisions to ensure that U.S. workers, agricultural producers, and firms can compete fully on fair terms and enjoy the benefits of reciprocal trade concessions, and to address and remedy market distortions that lead to dumping and subsidization.

(Sec. 529) Rescinds certain unobligated funds available to the Department of Commerce and DOJ. (Sec. 532) Prohibits the use of funds under this Act to: (1) transfer or release to or within the United States Khalid Sheikh Mohammed or any other detainee who is not a U.S. citizen or a member of the U.S. Armed Forces and who is or was held on or after June 24, 2009, at the U.S. Naval Station, Guantanamo Bay, Cuba, by the Department of Defense (DOD); or (2) construct, acquire, or modify any facility in the United States, its territories, or possessions to detain or imprison such a detainee.

(Sec. 534) Prohibits the distribution of funds to the Association of Community Organizations for Reform Now (ACORN) or its subsidiaries.

(Sec. 535) States that funds made available in this Act should be used to purchase light bulbs that are "Energy Star" qualified or have the "Federal Energy Management Program" designation.

(Sec. 537) Prohibits the use of funds under this Act to: (1) relocate the Census Bureau or employees from the Department of Commerce to the jurisdiction of the Executive Office of the President, or (2) maintain or establish a computer network unless such network blocks the viewing, downloading, and exchanging of pornography.

(Sec. 541) Establishes the Commission on Wartime Relocation and Internment of Latin Americans of Japanese Descent. Directs the Commission to extend the study of the Commission on Wartime Relocation and Internment of Civilians of U.S. relocation, internment, and deportation to Axis countries of Latin Americans of Japanese descent held in U.S. custody from December 1941 through February 1948.