I use Mindsystems Amode V2 for managing the overall PhD project. It’s not the only project management tool that I use but it sits at the top of my project management system hierarchy (see my other PM tools here). I have my entire project mapped out in it and I monitor its progress daily, amending the tasks and completing them. I put my main Amode file into Windows’s Startup folder, so that it starts up every time I restart the computer (it’s a way of having it in your face every morning).
The reason I chose Amode over other competent project management tools (and I’ve checked out a few – see the discussion surrounding the search process here) is that it is reasonably simple to use for a single personal project, such as a PhD dissertation (although Amode also can handle several open projects through its tabbed interface). Other PM software I found too bloated, as they try to cover every imaginable PM scenario from building bridges to organising NASA space missions. Amode on the other hand is sophisticated enough to give you the main PM functionalities (the Tree, which serves as the work breakdown structure, the Chart which is a proper Gantt chart, and the Calendar, which is integrated with the other two) but it’s also simple enough for everyday use. In fact I probably only use 10% of Amode’s functionality but I’m very happy with it as a PM tool.
I just noticed that Mindsystems uploaded a bunch of videos to YouTube about Amode’s features. Here is the project management module, so you can get an idea (actually it’s quite funny that it ends with the line: it “does not require a PhD to operate,” as I still don’t have my PhD :)
I thought it’s worth mentioning that if you are buying this software from outside of Australia, then you don’t have to pay their GST (tax), so the price should be considerably lower.