Well, we've used TestTrack for years now, which supports hierarchical linking between items. It's project management UI is nothing to write home about however.
It seems as though you're looking for something more like @Task, where you create a project plan using a system similar to Microsoft Project, with future tasks depending on previous tasks, etc. The UI is pretty slick, but when you get to the bug tracker you're pretty much back in "glorified spreadsheet" mode - i don't get the impression this was really designed by or for programmers. Still, might be worth a look if you're really serious about needing this.
IMHO, the problem with adding a hierarchy to your tracking system is that issues do not naturally have a hierarchy when they're added; someone in QA finds a regression, or a user calls in from the field, and an issue gets created. Until at least some research is done into the root cause of the problem, the issue is stand-alone, and chances are, it'll be stand-alone until it's fixed unless it's identified as dependent on some larger project... for which there is likely already some sort of a project management system in place.
