Hya nestor,
I haven't used GTD specifically for learning Japanese. I wanted to use it to manage my time better working on the site. I'm not using GTD anymore but I have kept some good ideas and continue to use them:
- I have what they call a "inbox", like a simple paper rack on my desk where I put all the bills, letters etc and clear them out whenever it suits me

It doesn't sound like much but already makes a big difference, simply to have many tasks grouped in one place, instead of leaving those all over the appartment as I used to. It does give some respite to the mind as with habit, you know you haven't put the "to do" paperwork anywhere else, so a quick glance at it and you know what's left to do, if any. Clearing that "inbox" feels good!
- I bought
files like this with a small box (nothing as drastic as that picture

). Organized a lot of old papers, bills to archive, ideas for the site, some documents or Japanese text I printed out, etc. Those act as archives, are always available but out of the way.
- Another thing I tried and found very useful is to split the mailbox in "Archive" "Follow Up" and "Hold", anything else is deleted. I still haven't got around to process all my old mail though. The idea there is to treat the mailbox like the "inbox", and go ultimately look at an empty mailbox.
Basically GTDhelped me organize myself better and also feel more relaxed instead of "scattered" because I know where the tasks are.
But otherwise GTD is very demanding, and hard to implement fully. I read that many times too, so I'm not alone. Several people who blog about GTD say they only truly implemented it into their life after a year or so. But anyway, like I said above, you can keep some good things of it, and the original GTD book makes you think and reconsider how you manage your time and your goals etc, so it's well worth checking out. Like me you will certainly keep something of it, even if you don't implement it fully.
If you implement GTD or part of it to your Japanese learning, keep us updated!
PS: Forgot about the software : I haven't used any software specifically tailored for GTD. I like to use
stickies for keeping thoughts and very simple lists of things, beautifully simple

You can configure it to show/hide your stickies with "Windows key + Shift + S" for example, you can paste links in the stickies too, etc.