GIS gives you the tools to excavate a site, digitize/record each stratum or level as it is removed, and rebuild a 3D virtual site. From the 3D model, you can view layers individually or in combination to compare data and identify spatial relationships. Using ArcGIS 3D Analyst, you can review site area and structure volume statistics.
Flyover of Petra in Jordan
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Mark Brender, Vice President Corp Comm/Wash Ops of Space Imaging (image); Dr. Talal Akasheh, Vice President, The Hashemite University, Jordan (digital elevation model and georeferencing);
Dr. Douglas Comer, Principal, Cultural Site Research and Management, Inc. (georeferencing)
GIS has most frequently been employed in archaeological studies for large-scale regional analyses and predictive modeling of settlement patterns and land use. ArcGIS Spatial Analyst gives you the capabilities to search for and uncover patterns.
Take a look at case studies, demos, and books and literature.