I use the methodology called Scrum when working on Tactics Ensemble. It’s very appropriate for any videogame project where there are a lot of unknowns at the start.
The most useful thing it can provide you is what they call the burndown chart.
It’s a chart detailing how many tasks you’ve done, and how many you should’ve done at the time. From there you can predict if you’re going to miss the deadline or not.
I use OpenOffice Calc with a bunch of formulae to help me automate much of the calculcations.
From the image you can see I was on a roll back in July. That was when I made melee attacks and the attack editor.
Right now I’m cutting it close, but the progress is good.