If you prefer to keep to paper, rather than transcribe everything onto your computer, then I think it's a case of investing in folders and box files.
I have large (A4 size) spiral bound notebooks in which I write notes, ideas, research etc. I don't attempt to put, say, all the medical research into one section of the notebook, but just start writing on the next available page so everything is in roughly chronological order (I try to date everything as well) -- though if I don't fill the entire page, I might add a later piece of medical research on the end there, if it fits. I number the pages as I'm going and keep a very rough index at the beginning of each book.
At the moment this works fine -- I can find things relatively quickly and easily, but I'm only just about to start my third notebook, so I might be singing a different tune by number ten! I had intended to keep each novel to one notebook, but that kind of slipped when I had to revisit number 1 to make amendments while number 2 was still being written -- but since they are part of the same series that isn't much of a problem. I think if I was embarking on a very different novel, I would have to start a new book and keep it wholly separate.
For printed out research and newspaper cuttings, photos etc I have a box file with different folders labelled appropriately eg medical, scientific, miscellaneous. At this point I don't have enough cuttings to warrant further sub-divisions, but obviously this is an option. These items are more for generating ideas than helping with plot etc, so it isn't so important to me to know what is in each folder, as I'm not needing to sort through them in a hurry. If it was necessary, then numbering the cuttings and preparing some kind of index would be the logical next step.
J