I have found a few Lewis & Clark GIS sites of interest. The first is from geodata.gov and is called the Lewis and Clark Geosystem, which is a collaboration of GIS technology and date from multiple organizations. Here is a summary from their description:
"Purpose: The purpose of the Lewis and Clark Geosystem is to provide multiscale and mutlitemporal examination of the geography of the Lewis and Clark trail. Covering two hundred years of change, 1803-1806, the purpose is to present a variety of spatial data, historical, ecological, climatological, etc., in a way that allows for examination of historical landscape change as a result of anthropogenic and non-anthropogenic effects. A second purpose is to explore the deployment and networking of a variety of geospatial Web services that each provide unique geospatial data types of interest to the study of the geography of the Lewis and Clark Trail. "
Also, there is the David Rumsey Lewis and Clark Historical Maps, with GIS. This is a commercial website, but to use the GIS is free. Resources: Lewis & Clark GIS Lewis & Clark Description Lewis & Clark Trail - National Park Service Lewis & Clark - Mapping the West
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