I use taskjuggler. It can do resource leveling, tracking and uses text files, i.e. you can generate tasks from bugzilla entries and store everything under revision control.

The thing with software is that it is usually asked to change "in flight". No one asks to have bridges changed after the building phase starts. That's not true with software. And things do get messy. That's the same reason why you can't use classical engineering methodologies with software.