Is there any reference management software that supports hierarchical tagging? At the moment I'm using Zotero to organize my paper collection and for my current work I'm very happy with it's possobilities to organize content (folders and tags).

However, working on bigger projects a hierarchical tag structure would come in handy where subtags can be assigned to lead-tags (or something similar). Is there any reference program that can do that?
JabRef is a reference manager using the BibTeX format. It uses the concept of groups, i.e. papers can be put into groups, and it allows to create a hierarchical group structure. Since one paper can be put into any number of groups, it is essentially hierarchical tagging.

With JabRef, one can even configure for individual groups whether a group will automatically include the content of any subgroups (analog to tagging), or will include the content of any supergroup (refining), or just include the papers assigned exactly to this group (as in a classical folder structure).