I have found that the following actually helps with the keeping things together in academia.

First thing is the book of course. For xmas each year, I give my new graduate students their own copies. Since you are posting here, you probably already have the book, but I also think it helps to reread it every 6 months or so until GTD becomes a habit.

Second, I personally find that relying on a single tool or piece of software for implementing GTD for academics is like trying to force square pegs in round holes. Instead, I like to have individual tools that focus on one sphere of activity. For example, in writing a thesis (disseration, grant proposal, class assignment, class prep) you will have lots of pieces of information to keep integrated. Something like Freemind is great for this. I reckon a GTD purist would say that all these pieces of information are REFERENCE items, but I haven't found a good piece of GTD software that handles this type of information very cleanly - along with the rest of the GTD system.

For implementing the rest of the GTD system there are many different pieces of software (ahem..), paper based systems, pda systems, etc, that you can choose from. My only advice here would be find the one you feel most comfortable with and STICK WITH IT. It is very tempting to keep switching systems (they can be fun to explore) - but that brings new startup costs.

Since what I'm suggesting (Freemind for writing/references and something else for the rest of GTD) relies on two different tool sets, it is very important that you be able to crosslink between the two. This is easily done with Freemind.