For basic GTD organization, I use a homegrown system that I've mocked up in my Primary Voodoopad document. It's mostly just me, and my copy and paste buttons, but I like that it's in the same document that I for nearly everything, so there's no stress, I don't loose things. The downside is that I have to transport everything myself, and I don't get nifty dynamic lists. Perhaps someone else will develop some sort of VP solution that I could partake of, but I like my system pretty much.

For articles and documents, I've thought about using some sort of database/citation, and I've tried a number that are pretty nice, but that don't seem to quite make it work. I keep folders based on both courses I've had and on general interests/themes that I tend to find articles for. This means that if I'm looking for an article I can generally find it based on whatever context it came to me in. If this were paper, it would be a crappy system, but as it is, between Spotlight and Quicksilver, I can find anything with great speed, and the filing is irrelevant. The key thing is to put enough useful information in the spotlight comments for articles from sources like Jstor where the text is actually an image. I've also started putting some things thatd I use more frequently, or that are more project specific, in my voodoopad, but again, spotlight and quicksilver can get at those files, so it doesn't matter as much. Some sort of automatic or dynamic citation management would be awesome, but you can't get everything.

Cheers,
sam