MavenLink is rather nice. For long-running projects, I think something with Gantt charting is an absolute necessity and most programmer "issue trackers" don't have Gantts. But this is mostly due to their mapping to methodology. Gantts come from waterfall methodologies and that doesn't settle with an agile process.
Software works well for agile processes but there are a lot of tasks and projects out there that are much more tuned to waterfall methods. Long-running projects, for example, can have tons of dependencies. Dependencies don't exactly play well in the agile process.
In the end, I think a combination of the two works well for some organizations. Waterfall / Gantt / MavenLink works well for the big-picture view where teams work concurrently and sequentially. Agile works well for small-grained tasks that are too numerous or tedious to incorporate into the waterfall view.