I'm a Linux user (I'm a programmer) and I just read the "Getting Things Done" book and I am quite impressed with it. I looked around for a software solution, but couldn't find anything I really liked. Then I came across this site: http://www.rememberthemilk.com/
This is a "web 2.0" site and it supports xml and rss feeds so you can integrate it with whatever application that supports these protocols (ie, Mac or Palm or Linux or whatever). You might want to try this app as it seems to be conducive to what David Allen likes.
But yeah, it integrates with whatever application on whatever platform you prefer.