Victor provides a bunch of good links on the SIGIA list for when you need to align metadata between a bunch of different systems:

Basic introduction to what and why
Examples
Mapping Between Taxonomies
Semantic Problems of Thesaurus Mapping
Issues in Crosswalking Content Metadata Standards

I would definitely suggest looking into TopicMaps when you need to merge a bunch of systems metadatawise! Really, do it. They are very cool.