To date, I have been using Thinking Rock for GTD. It's an excellent application, I believe it's the most advanced and, at the same time, the most intuitive software tool for GTD. Unfortunately, it has a big problem: it's a desktop application, there is no support for using it on multiple computers at all.
I have been trying to work around this problem for months: first, by keeping its data file on a USB stick, then by using Dropbox. It kinda worked, but I had to remember to shut Thinking Rock down before putting the computer to sleep; otherwise, when the computer was waked, it worked on its in-memory data and after a while saved it thus overwriting changed made on other computers. Dropbox keeps old revision of the files it manages for 30 days, so it was all too easy to recover those changes, but so was it frustrating.
This made me look for a new tool. It had to be either a webapp, or a desktop app able to run on Windows and Mac, and with synchronization support.
The first shot, Chandler, I dismissed almost at once. It felt almost like an old school PIM, not a simple app for GTD. On the other hand, it has its own synchronization protocol and a free server for online data, so it might be worth a try for some.
Then came RememberTheMilk. Looks nice, but authors seemed to be a little carried away with adding locations (we use Google Maps, we're trendy), tags and other Web2.0 stuff, much less proper GTD stuff like projects, goals, visions, not even contexts (which I believe are expected to be simulated with locations and/or tags).
I've also read about Nirvana. Looks promising, but that's it for now. I wish they launched so I could try their services.
Then I found gtd-php. A simple, open source webapp whose authors seem to have read and understood the book. I migrated my current data and it is really nice to use it. There are some disadvantages: it requires MySQL, though SQLite would do just fine, it requires a webserver and it has no security features, not even user login. It might also be quite hard to install for a non-geek. Otherwise, I really like it. (They also have an online demo. Too bad, no security features means the demo was all too easy to spam. However, I still think it's worth playing with.)
First, it's simple. Add inbox item, add action, add next action, add project and that's all (it's sometimes quite counter-intuitive, e.g. to add an action to a project you have to click "Actions" link looking like a section header). But it isn't too simple. There is still support for contexts, goals, projects and so on.
There's a very nice screen "Weekly review" which might be of great help to GTD beginners, and not just beginners. It lists every step that one should take during a review, and, if something is missing, like the next action for a project, it's also listed there. Although I have been practising GTD for three years now, I'm glad there's this list and I will surely use it. (And yes, I'm gonna add those missing next actions as soon as I'm finished with this post.)