Minion is a product quality search engine written in Java, created by Oracle Labs. In addition to standard document retrieval operations, it provides for relational querying in conjunction with boolean and proximity querying. It also provides document similarity measures (e.g., "More like this"), result and document clustering, and automatic document classification. The engine is designed to be highly configurable/pluggable and is intended to be used in research as well as production environments. We're still putting documentation together, but here are a couple links to help you get started.
Summary of Features

Indexing & Retrieval
Classification
Clustering
Configuration
Performance