On our website for a cancer-related organization, we have a flat tag structure with tags like "Leukemia" but also "Chronic Myelogenous Leukemia" and "Acute Lymphoblastic Leukemia". We have a rule that anything tagged with a specific kind of leukemia should also be tagged with the main "leukemia" tag, but there is no programmatic link between them.
It'd be nice if there were such a link--some relation between tags describing one as being a parent/child of another--so that on, say, the "Leukemia" page we could have some links to the sub-topics: AML, CML, etc.
It look like the developers don't plan on supporting this (according to a Jan 2011 github issue), but it seems like a common enough use case that maybe someone's found a workaround, perhaps by modifying the Tag model to make tags themselves taggable (insert Xzibit photo).