I have a system like Rosy's--piles of related things. How they relate sometimes changes, and then the piles get re-arranged. It is a bit like archaelogy at times, going on a big dig. This is all complicated by my overseas move. I brought one case completely heaving full of books and articles--but left even more behind... I had to select which ones I needed the most, or would be difficult to access over here in the UK.
Actually--it works---for some reason I seem to have good recall even months later, that so and so did an article on such and such, and can locate the article and go on from there.
I think my lowest moment in organization was when my darling male puppy showed off one of his developmental milestones, lifting his hindleg and having a wee all over a stack of articles...