So, my own personal biggest issue with Getting Things Done is that it seemed a little old hat, with paper filing or PDA's recommended, it felt a little 20th Century. I love using the latest technology and software because for me it saves me lots of time and helps me be more organised.
So, my main tool of choice for Getting Things Done is an app called Wunderlist. I can access it from anywhere, on any device, and I can set dates for when things need doing, incubate tasks and generally know what needs doing and when. It's biggest help, was it helped me get down the thousands of ideas from my head onto an actual list that would make sure they got done, saving time, sleep and letting me focus on the bigger picture. Now I can add things while sat at my desk, or if I'm out I can add them via voice using Google Now on my phone.
The only issue with Wunderlist is that it's hard to specify all the sub-actions to any one task, which is particularly difficult for projects. So, for that reason I'd also recommend using Asana, where you can put flow through projects together and also collaborate as a team for getting these bits done, while a simple task on Wunderlist will specify what it is and when it needs doing.