Homeless Emergency Assistance and Rapid Transition to Housing Act of 2008 - (Sec. 3) Amends the McKinney-Vento Homeless Assistance Act to redefine "homeless, homeless individual, or homeless person." Includes in such definition not only a family lacking a fixed, regular, and adequate nighttime residence, but also an individual or family who: (1) will imminently lose their housing; (2) has no subsequent residence identified; and (3) lacks the resources or support networks needed to obtain other permanent housing. Includes as well an individual who resided in a shelter or place not meant for human habitation and is exiting an institution where he or she temporarily resided. Expands the scope of such definition to include unaccompanied youth and homeless families with children and youth defined as homeless under other federal statutes who: (1) have experienced a long-term period without living independently in permanent housing; (2) have experienced persistent instability as measured by frequent moves over such period; and (3) can be expected to continue in such status for an extended period of time because of chronic disabilities, chronic physical health or mental health conditions, substance addiction, histories of domestic violence or childhood abuse, the presence of a child or youth with a disability, or multiple barriers to employment. Requires the Secretary of Housing and Urban Development (HUD) to consider as homeless any individual or family who is fleeing, or attempting to flee, domestic violence, dating violence, sexual assault, stalking, or other dangerous or life-threatening conditions in the individual's or family's current housing situation, including where the health and safety of children are jeopardized, and who have no other residence and lack the resources or support networks to obtain other permanent housing. (Sec. 4) Declares that the mission of the U.S. Interagency Council on Homelessness is to coordinate the federal response to homelessness and to create a national partnership at every level of government and with the private sector to reduce and end homelessness in the nation while maximizing the effectiveness of federal contributions to end homelessness. Adds to the membership of such Council the Commissioner of Social Security, the U.S. Attorney General, the Director of the Office of Management and Budget (OMB), the Director of the Office of Faith-Based and Community Initiatives, and the Director of USAFreedom Corps, or their respective designees. Requires: (1) the Council to meet quarterly (currently, annually); and (2) rotation of the position of Chairperson and Vice Chairperson at the first meeting of each year. Directs the Council to develop, make available for public comment, and submit to the President and Congress a National Strategic Plan to End Homelessness, to be updated annually. Increases the number of regional coordinators employed by the Council from between two and five to between five and 10. Requires the Council to: (1) encourage state and local governments to develop 10-year plans to end homelessness; and (2) develop constructive alternatives to criminalizing homelessness and eliminate laws and policies that prohibit sleeping, feeding, sitting, resting, or lying in public spaces when there are no suitable alternatives, result in the destruction of a homeless person's property without due process, or are selectively enforced against homeless persons. Authorizes the Council to: (1) arrange national (currently, federal) conferences to develop and coordinate effective programs and activities to assist homeless individuals; and (2) pay for expenses of attendance at meetings regarding the functions or activities for which the appropriation is made. Authorizes appropriations for FY2009-FY2010. Title I: Housing Assistance General Provisions - (Sec. 102) Prescribes requirements for a collaborative homeless assistance grant applicant for a geographic area, which shall: (1) design a collaborative process for applying for housing assistance; (2) participate in the Consolidated Plan for the geographic area served; and (3) ensure operation and participation in a communitywide homeless management information system (HMIS). Authorizes collaborative applicants to become unified funding agencies responsible for distributing funds to grantees and ensuring proper accounting methods. (Sec. 103) Prohibits any project sponsor receiving funds to provide emergency shelter, transitional housing, or permanent housing to families with children under age 18 from denying admission to any family based on the age of any child under 18. Makes an exception to this prohibition for project sponsors of transitional housing which target transitional housing resources to families with children of a specific age, if the project sponsor: (1) operates a transitional housing program that has a primary purpose of implementing an evidence-based practice that requires that housing units be targeted to such families; and (2) provides assurances that an equivalent appropriate alternative living arrangement for the whole family or household unit has been secured. Directs the Secretary to make technical assistance available to private nonprofit organizations and other nongovernmental entities, states, metropolitan cities, and both urban and nonurban counties to: (1) implement effective planning processes for preventing and ending homelessness; (2) improve their capacity to prepare collaborative applications; (3) prevent the separation of families in emergency shelter or other housing programs; and (4) adopt and provide best practices in housing and services for persons experiencing homelessness. (Sec. 104) Requires the Secretary to instruct a victim service provider that is a grant recipient or subgrantee not to disclose for HMIS purposes any personal identifying information about any client. (Sec. 105) Authorizes appropriations for FY2009-FY2010. Title II: Emergency Solutions Grants Program - (Sec. 201) Renames the Emergency Shelter Grants (ESG) program the Emergency Solutions Grants Program. Directs the Secretary to allocate nationally 20% of homeless assistance funding for specified activities. Allows a grantee to use up to 60% for traditional shelter and street outreach activities. (Sec. 202) Specifies among eligible activities short- or medium-term rent assistance, and new homelessness prevention and housing relocation and stabilization activities. (Sec. 203) Requires the Secretary to ensure that Emergency Solutions Grants recipients ensure the consistent participation by emergency shelters and homelessness prevention and rehousing programs in any applicable communitywide HMIS. Title III: Continuum of Care Program - (Sec. 301) Consolidates the Supportive Housing and other specified existing programs into the Continuum of Care Grant Program, whose purpose is promoting commitment to ending homelessness, rehousing homeless people, minimizing the trauma of homelessness, helping people access mainstream services, and optimizing self-sufficiency. Permits the Secretary to award grants to solo applicants but only if they have attempted to participate in the Continuum of Care Program and were not permitted to participate in a reasonable manner. Grants flexibility to a collaborative applicant to serve persons defined as homeless under other federal statutes. (Sec. 302) Specifies eligible activities under the Continuum of Care Program, including construction, acquisition, rehabilitation, leasing, rental assistance, operating costs, supportive services, rehousing services, and HMISs. Requires projects receiving funding for construction, acquisition, or rehabilitation to be used for their intended purpose for at least 15 years. Authorizes conversion of a project no longer needed for its intended purpose in order to benefit low-income people directly. Requires the grantee of any project needed but not used to serve homeless people for between 10 and 15 years, except under certain conditions, to repay all or a portion of the grant. Requires permanent housing rental assistance to be administered by a state or local government or a public housing agency. (Sec. 303) Prescribes incentives for high-performing communities, including flexibility to serve persons defined as homeless under other federal statutes. (Sec. 304) Revises supportive housing requirements for grantees. Requires them to: (1) designate a staff person to be responsible for ensuring that children being served in programs that provide housing or services to families are enrolled in school and connected to appropriate services in the community such as Head Start, the Early Intervention Program for Infants and Toddlers with Disabilities, and programs to educate homeless children and youth; and (2) place families with children as close as possible to their school of origin so as not to disrupt their education. (Sec. 305) Revises grant selection criteria and prescribes fund allocation formulae for the Continuum of Care Program, as well as incentives for proven strategies and their successful implementation. Requires the use of Section 8 (rental assistance) funds for renewals of expiring contracts for leasing, rental assistance, or operating costs for permanent housing. Prescribes requirements for matching funding. Directs the Secretary to establish an appeal procedure for denied certifications. (Sec. 306) Authorizes appropriations for FY2009-FY2010 for research into the efficacy of interventions for homeless families, to be expended over two years at three different sites to provide services for homeless families and evaluate the effectiveness of such services. Title IV: Rural Housing Stability Assistance Program - (Sec. 401) Revises and renames the Rural Homeless Assistance Program the Rural Housing Stability Assistance Program. Requires the program to: (1) rehouse or find housing for people who are homeless or in the worst housing situations; (2) stabilize people in imminent danger of losing their housing; and (3) improve the ability of the lowest income residents to afford stable housing. Adds to the list of eligible Program grant uses construction, acquisition, rehabilitation, leasing, rental assistance, and payment of operating costs for transitional or permanent housing for homeless people. Adds to application requirements a description of: (1) consultations to determine the most important uses of funding; and (2) the nature of homelessness and the worst housing situations in the area. Sets a uniform 25% cash or in-kind match requirement for the project or activity; except that grants for leases shall not be subject to matching requirements. Directs the Secretary to establish criteria for selecting grant recipients, including specified requirements. Defines a rural area as any place outside of a metropolitan statistical area or any census tract within a metropolitan statistical area that is at least 75% rural. Considers any state with fewer than 30 people per square mile and at least 1.25% of land under federal control to be rural in its entirety, provided that no metropolitan city is the sole beneficiary of the grant. Prescribes requirements for the funding process for the rural program. Allows a rural applicant to apply under the Continuum of Care Program or the Rural Housing Stability Program. Requires that, if the Secretary receives applications from the same rural area under both programs, the Secretary must first seek agreement from the applicants about how to proceed, or, in the absence of agreement, must fund the application that would result in the most funding for the geographic area. (Sec. 402) Requires the Comptroller General to study and report to Congress on homelessness and homeless assistance in rural areas and communities. Title V: Repeals and Conforming Amendments - (Sec. 501) Repeals provisions of the McKinney-Vento Homeless Assistance Act: (1) establishing the Safe Havens for Homeless Individuals Demonstration Program; (2) providing Section 8 housing assistance for single room occupancy dwellings; and (3) establishing the Shelter Plus Care Program. (Sec. 502) Makes other conforming amendments to such Act.