I am running a private installation of redmine.
It has projects (and sub-projects), an RBAC system, issue tracking (and each project can have multiple "trackers" associated with it), milestones, file management, per-project wiki and forums, time tracking (with Gantt charts), it supports LDAP, multiple languages and multiple databases and has a nice e-mail-based interface to manage issues, if you need it.
It is also integrated with the most popular VCSes (Git, SVN, Bazaar, Darcs, CVS): other than providing a repository browser (+diff viewer) you can close tickets by putting some special text (e.g.: "closes #10") inside your check-in comments.
It might not be as complete as commercial alternatives but it's an over-the-average open source web application in this field.