I use Microsoft Project. The key with Gannt charts though is not the software, but actually knowing what you are doing in terms of project management. See if there is a good project management course at your uni for free (there was here) and then actually apply it! The software is just a tool. For PhDs with usually just one person working on the project Microsoft Project is slightly over kill, but I know how to use it and it keeps me used to it for the future (jobs after PhD etc).
The other software I use is FreeMind for Mind Maps.
I also have a large A2 pad for if I need space to work stuff out and I make use of a white board in my office for the same reason.
I used to put tasks on a note on my desktop (windows 7) but I don't do that now.
My tomatoes is good when I need a kick up the arse to get going.