The Google Search Appliance is designed for larger businesses and can support up to 30 million documents. The Search Appliance includes a number of unique features, including direct database indexing, a feeds API allowing you to push new content into the index, query stemming, RAID (to provide continued service in the event of hard disk failure) and deeper support for user-level document security, including a security API. These features are unique to the Google Search Appliance.
For more information, see the comparison chart at: http://www.google.com/enterprise/feature_comparison.html