Getting Things Done is by far the most influential book I've read. It has changed the way I think about everything. However, I have never been able to find a good implementation of the system. I know that David Allen (GTD) and Charles Simonyi (Intentional Software) were working on something at some point, but I haven't heard anything since.
1. ThinkingRock
It's a desktop client for all operating systems. There are two versions. A free one (v 2.x - still available on sourceforge [0]) and one you have to buy (v 3.x)[1]
2. Getting Things Gnome
I find it slightly less convincing than ThinkingRock. What's more, it appears not to be maintained anymore. The offical website is down and there have been no update on github[2] for a while. However, it might be just what you're looking for so you should also give it a try.