Sesat: http://sesat.no/

Google Search Appliance
http://www.google.com/enterprise/search/gsa.html
— has alerts
— PKI enabled

Google Mini
http://www.google.com/enterprise/search/mini.html
— no alerts

DeepWeb — This one might be a fit – it has an alerts feature
http://www.deepwebtech.com/

Carrot2 is a Results Clustering Engine — it groups searches into topical groups
— this is not a solution, but if we build something, it might be a part
— written in Java, but easily accessible from other languages
http://project.carrot2.org/

Microsoft FAST ES (was FAST Unity)
http://www.microsoft.com/enterprisesearch/en/us/Fast.aspx

dbWiz — this is opensource, did not see alerts / repeatable searches
          — targeted at Libraries
http://researcher.sfu.ca/dbwiz

WebFeat — seems very targeted to libraries
http://www.webfeat.org/

http://en.wikipedia.org/wiki/Sesam

http://en.wikipedia.org/wiki/Federated_search

http://en.wikipedia.org/wiki/Metasearch_engine

http://en.wikipedia.org/wiki/Focused_crawler

http://en.wikipedia.org/wiki/Web_crawler

http://java.sun.com/developer/technicalArticles/ThirdParty/WebCrawler/