The best planning tool I've ever used is also the most low-tech. It's a set of story cards, a big table, and a six-foot, magnetic (steel-backed) whiteboard on wheels.
Let me set some context: I've found the XP approach to planning to be very successful. Writing stories on cards, estimating them, and spreading them out on a table for prioritization is the most effective approach to project planning that I've yet seen.
It's effective because in addition to giving you a timeline, it requires everybody to be in the same room and talking to each other. It allows everybody to reach in, grab a card, and move it around. In practically forces people to face disagreements about priorities and schedule head-on.
I've seen some common failure modes. The biggest, by far, is computerizing the process. As soon as you computerize the planning game, you lose what makes it effective. People no longer need to be in the same room. Even if they are, there's one person in charge of the projector. He or she is the only one who can make changes.
With computerized planning, it becomes way too easy for people to be wallflowers, saving up their complaints for later. And, in fact, that's what I've seen happen.
Outside of the planning game, whiteboards have a big advantage over computers. They're much, much higher resolution. They're always visible. They convey general information about progress from a distance and specific information up close.
When there's a big planning board present, people will sometimes wander over and just stare at it while they're taking a break. Sometimes this brief zone-out period will result in an ah-ha moment or other discovery. I've never seen that serendipitous behavior with computerized plans. With a computer, you need to make a conscious effort to go look at the plan. You don't have a six-foot whiteboard that's always visible.
Computerized planning tools also put far too much emphasis on tracking individual tasks. The best measure of progress is Running, Tested Features (as Ron Jeffries so eloquently describes). Although I see value in tracking progress throughout the iteration, the computerized tools I've looked at place disproportionate emphasis on task tracking... perhaps because it's easy to do.
Instead, I prefer to simply mark tasks "done" when they're done. If I use a whiteboard and I circle each card green when I've finished it, I have a nice, visual indication of how far along I am. Halfway through the iteration, about half the cards should be circled green. Simple... and visible from a distance.
(Note: This works because I plan small tasks: tasks are only a few hours long and stories are usually only a day or so. This varies depending on the size of the team.)
There is one thing that a computer can do that a cards, table, and whiteboard cannot, and that's deal with distributed teams. I would be very interested in a tool that helped teams that have a few distributed customers or stakeholders. Such a tool would act as a supplement to cards, table, and whiteboard, rather than a replacement for it.
How would this work? I'm not sure. Perhaps it would integrate a webcam, or provide a virtual set of cards, planning table, and whiteboard. However it worked, it would assume that people used it primarily to collaborate along with a conference call. It would show changes in realtime to all participants.
I haven't seen such a tool yet. When I do, that'll be computerized planning tool I recommend. But even then, for a co-located team, cards, table, and whiteboard are king.