Iowa has a unique status among state archives of having both very little and very comprehensive information online.
Iowa State Historical Society, has links to a number of smallish collections:
Some interesting topics, to be sure, but as I said, the collections are generally modest in scope.
However, for some mysterious reason, Iowa has some of the best free newspaper archives available online, allowing users to search through millions of articles covering the history of the state:
Few states offer such a rich online collection of fully searchable newspapers, so take advantage of Iowa's special crop.
Update! Turns out the University of Iowa hosts a pretty nifty archive of their own, the Iowa Digital Library. Not everything here is strictly Iowa-related, but then again, much of it is! Definitely worth an explore.