I've used Mantis in many organistions and particularly because of the sub-issue feature which is one of my key points I look for in an issue-tracker. They have Freemind export in Mantis now but I'm sure I've seen parent-child diagrams drawn at one site, maybe because they installed JpGraph.
I'm also using the free single-user install of Axosoft's OnTime system which has very flexible sub-issue entry although the UI is a little clunky - you have to search for issues rather than being able to specify a given issue number directly as the target of the relationship. OTOH it allows you to configure a bunch of relationships in one hit in the dialog so is quicker in that scenario.
