We've given up on using MS Project to do project management (for software development) and we're currently evaluating a couple of different (though not free or open source) web-based task tracking systems.
The company I'm at used to use Project, and had gantt charts coming out the wazoo. Useless as tits on a bull, since none of them were ever accurate, and we were always behind schedule. Our department has shifted to the Agile/scrum stuff. You can get software to run the scrum process, but the low-tech method is just index cards tacked to the wall, which, I have to say, I'm really digging.
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