In this case, the plugins turned out to be workflow plugins. That is, plugins that are used to extend the workflow (or Process in CRM 2011 speak) functionality.
The error message that was shown contained some text that looked like this:
>Crm Exception: Message: The PluginType(a222ddda-c78e-45c8-91f9-fa06359ac29d) component cannot be deleted because it is referenced by 1 other components. For a list of referenced components, use the RetrieveDependenciesForDeleteRequest., ErrorCode: -2147160033
[2011-12-06 12:03:51.118] Process: w3wp |Organization:9dd6ac5e-4be6-46f9-af58-7caed1001d66 |Thread: 31 |Category: Platform |User: 6b51be4f-7308-dc11-9e28-00188be6f91e |Level: Info | MiniDump.CreateDumpInternal