Don't know a lot about this but here's an 'In-general explaination of "the difference" -Appears that AS9100 is the latest version of AS9000 - Have you checked with ASQ? or a registrar for details?
About AS9100
AS9100 is an international aerospace standard for quality assurance in design, development, production, installation and servicing. AS9100 was developed using ISO 9001, AS9000 and EN9000-1, and succeeds the AS9000 standard by building upon the requirements to produce a harmonized standard that meets the requirements of aerospace companies worldwide. AS9100 is the first single standard accepted by and available for use across the global aerospace community. Additionally, AS9100 incorporates the requirements necessary to address both, civil and military aviation aerospace needs.
About AS9000
AS9000 was published by the SAE (Society of Automotive Engineers) in May 1997. Developed by major aerospace contractors such as Boeing, Pratt and Whitney, GE, Lockheed Martin, Northrop, and others in the industry, AS9000 is Aerospace specific, and includes all of the requirements of ISO 9001 verbatim. In addition, there are 36 supplementary items that address how ISO 9001 applies to the aerospace industry.