ALWAYS CHECK OUT THE U.S. GENWEB PROJECT. 1. choose your state link where you will find state wide resources, news, projects 2. each county has a web of its own - choose the county link also go to the GenWeb Archives and choose a county.  The archives are transcriptions of records that people have transcribed or abstracted and donated for others to use.  If the county you are working in is spare, check out all its neighboring county pages as many times a very active site will include records from surrounding areas.

American Local History Network: Iowa
Iowa at RootsWeb
Iowa Biographies Project
Iowa Databases at Rootsweb


Iowa at Ancestry - you have to have a paid subscription to see the records but this will show you what they have access to

LDS Family History Catalog Search  (do a place search by state or county or town etc. to see what has been filmed)

Archives, Libraries and Organizations

Iowa Genealogical Society
Iowa Pubic Libraries - they also have links to other types of libraries in the state

Census

Church

Historical Sketches of Iowa Baptists by S. H. Mitchell, 1886 [Google Books]
Iowa Church Records Porject (USGW)
Little Brown Church (Chickasaw Co., IA)
Presbyterian Church in Iowa, 1837-1900 by Joseph W. Hubbard, 1907 [Google Books]
Quakers in Iowa by Louis Thomas Jones, 1914 [Google Books]

Geographic

Iowa Counties Historic Atlases  DONT MISS! from the University of Iowa Digital Library
Iowa Maps:Perry Castaneda Library
Rootsweb Town Search enter the town and it will tell you its present day county
note that most Iowa Genweb pages include a township map of the county.

Guides

FamilySearch Wiki Guide to the States - constantly growing wiki with research help, ideas, links, knowledge
 Iowa Courthouse Directory from Genealogy.com
Iowa Genealogy Research Basics

History

Amana Heritage Society
Farmer's Index for SW Iowa Counties, 1892 - Cass, Fremont, Mills, Montgomery, Page, Pottawattamie & Shelby Counties
Iowa County Histories Online
Iowa Heritage Digital Collections

Land

Iowa Land Records Collection
Iowa Land Records Research Directory
Land Patent Search - BLM GLO Records. -  Bureau of Land Management original patents for Public Domain Lands 

Immigration & Migration

The Irish in Iowa
Norwegian Heritage in Story Co. & Central Iowa

Military

Black Hawk War of 1832 from the Abraham Lincoln Historical Digitization Project
Civil War Archive: Iowa
Iowa Civil War Regiments, Rosters and Muster Rolls [Access Genealogy]
Iowa Forts

Newspapers

Kidon Newspaper Directory: Iowa
Newspapers at the State Historical Society of Iowa (which may be inter-library loaned) Iowa
Old Press onine newspaper clippings from early papers

Vital

Iowa Vital Records Information

Marriages
Iowa Marriage Project from the U.S. GenWeb

Deaths

Cemeteries
Cemetery Junction: Iowa
Cemetery Records Online: Iowa
CemSearch Iowhttp://www.obitcentral.com/cemsearch/ia-cem.htma
Find A Grave choose the link on the top right column to search entries
 Iowa Cemetery Records from I Dream of Genealogy
Iowa Graves Registration Survey (WPA)

Obituaries
Iowa Obituary Links
Iowa Obits at the Iowa GenWeb