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Commercial Sites:

Ancestry.comthe best paid subscription site I have found so far
Genealogy.comalso a good subcription site
Familytreemaker.comthe genealogy software that I use

People Search: Genealogy ResourcesAn excellent resource of articles, information and links about genealogy research
Trace Your Family Roots From Immigration to US Citizenship: a Genealogy GuideAn excellent resource of information related to genealogical research
USGenWeba great resource for information at state and county levels
Online death indexesan excellent directory of online death indexes by each state
Chronicling America from the Library of Congressa collection of newspapers that have been digitized and are indexed online from across the United States
DAR Genealogical Research Systeman online index from the Daughters of the American Revolution of Revolutionary War patriots and their descendants.
US Geological Surveya good source for geographical information, maps, county names, etc.
Rootsweba good general genealogy website
Cyndislistalso a good "catch all" of genealogical info
Random Acts of Genealogical Kindnessa great site if you are looking for genealogical lookups
Familysearch.orgthe Mormon church's genealogical website which contains a large amount of free online data
Land Patent Recordsthe Bureau of Land Management's website which contains much useful information on early land records
1895 Atlascomplete atlas of the United States at, state and county levels
Stevemorse.orgmany helpful "one step" databases and genealogical links
Individual family/surname:

Barklowresearch of Thomas Burklow and Steve Bartlow
BarklowJim Barklow's website
BrooksThe Brooks Historian
Brower'Cowboy Johnny's' Brower family pages (and other related Dutch-American families
BrownDebbie Holtzendorff's Brown resources page, with many different Brown genealogies.
CannonCharles Cox' genealogy website
ChristmasChristmas family website
DowComprehensive genealogy of all the Dow families
DuncanDuncan Surname Association
DunhamDunham-Singletary research
DunsmoreDunsmore family research on the Boylston archives website
FoustFoust/Faust family of Germany, Pennsylvania and North Carolina
FossFoss pages of Kristin C. Hall's website
GeorgeMarty Grant's George family website
HatfieldHatfield family website, by Jerry Hatfield
HullHull Family Association
HuntHunt family archives by Courtney
HuntA collection of Hunt letters written in the 19th century
HusseyDetailed information on Christopher Hussey
HuyckDescendants of Hendrick Huyck
JamesonEdna Barney's Jamesons of Woods Gap and their Scottish Forebears
JamesonAnother Jameson family website
JonesJones family of Virginia
MarstonDick Marston's Marston (and related surnames) website, which contains many early families from Hampton, New Hampshire
MartiauNicolas Martiau Descendant Assocation
MorrillComprehensive Morrill genealogy website
Morsethe Morse Society's website
PhelpsPhelps Family in America History
PlymalePlymale family webpage
RiceEdmund Rice (1638) Association
RockwellRockwell Family Foundation - link not working, Jan. 2009
SinclairSinclair family website
ThurstonD. James' Thurston Genealogies website
TreadwayThe Treadway Web
TrueComprehensive True family genealogy with pages on many related families
UpshawThe Upshaw Family Genealogy Page
Van Der VeerVan Der Veer / Vandever genealogy website
Van ValkenburgThe National Association of the Van Valkenburg Family
WhitlockThe Whitlock Family Association
WhitneyWhitney Research Group
WillitsWillits family on a Mercer Co., IL website
WoodsonWoodson line from from a book on the ancestors of Charles and Mary Morton
WymanWyman Genealogy
Location specific:

Dansk Demografisk Databasethe Danish Archive's online records including emigration and census information

New England:

Ray's PlaceA nice collection of New England records that are online
Dunham-Wilcox-Trott-KirkIncludes a very large collection of New England vital records
Essex Co., MA GenWebA collection of many Massachusetts town vital records online (most from Essex and Middlesex Counties)

Western states:

Washington State Digital Archivesfrom the Washington State Archives
Heritage Trail PressOregon specific subscription site
Oregon Historical Records Indexa large online database from the Oregon State Archives
Rogue Valley Genealogical SocietyContains many helpful indexes
Southern Oregon HistoryBen Truwe's varied and fascinating sources of Southern Oregon (primarily Jackson County and Medford) history.
Genealogical Society of Douglas County (Oregon)
Western States Marriage Indexfrom the BYU - Idaho website
Vital Search CaliforniaCalifornia vital records
Siskiyou Cemeteries CentralSteve and Laura Melton's website that is now run by Rhonda Hammer. Excellent material for Siskiyou County, California.
Colorado State ArchivesDigital Archives page which contains a large database of indexes

Mid-Atlantic States:

Delaware County, New York Genealogy and History
Olive Tree Genealogyfree databases
Albany and Eastern NYCliff Lamere's helpful links and databases on Albany and the Eastern NY area
Sampubco.coma service that will provide copies of wills and other records for a fee, it also serves as a good index to will records, mostly in New York State
Delaware Co., NY GenWeb
Original 13 Settlers of Germantown, Pennsylvania

Midwestern States:

Missouri State ArchivesIncludes many indexes and databases
Indiana State Librarycontains many useful indexes
Boone Co., IN GenWeb
Jefferson Co., IN GenWeb
Illinois State Archivescontains a great deal of useful information and vital records from the state of Illinois
Sangamon Co., IL GenWeb
Winnebago Co., WisconsinJan Cortez's comprehensive Winnebago County website
Minnesota Historical Societycontains a birth and death index
Blue Earth County Historical Societycontains an index of all the known cemeteries in Blue Earth County

Southern States:

Tennessee State Library and Archiveswhich includes a Tennessee Death Index for 1908-1912 and 1914-1928.
Shelby County [TN] Register of DeedsIncludes a Tennessee Death Index for 1949-2005 and other indexes specific to Shelby County.
Folks Findersa site with some very useful information and family history on Montgomery Co., Tennesse
Christian Co., KY GenWeb