I never once have regretted tossing out any piece of paper that can easily be located in the library or on Westlaw. If you save all that stuff, you will spend more time saving it than you spend using it and, even then, it will be harder to find it when you need it than it would be if you just went back to the library.
The most important knowledge winds up in your head
From the spelling of "organise" I guessed the OP is a Brit - confirmed from his website. I just finished 2nd year of medicine (=1st clinical) in London and like the OP (and unlike most UK students) did an undergrad degree first. I had exactly the same issue as the OP last year.
The OP's post about his difficulty deciding how to categorise malaria doesn't really make sense to me. I decided on a filesystem structure by date supplemented by my brain, as I associate topics by when they were taught. So Malaria.pptx comes under Year 1 / Term 2 / Infectious diseases for me. If there are any papers, vidoes, etc. they go in the same folder with a sensible name. I do keep lots of papers, but I have barely had time to read most of them. What I do is summarise the abstract and citation into my own notes.
As the parent says I have actually spent more time sorting out these files than reading them. I don't think I would ever need to read those papers again except for interest, and I would find which one I wanted by checking the citations in my notes. I haven't even touched last year's notes. I have maybe touched the Year 1 folder twice this year, and had no problem finding the (powerpoint) file I needed. Yes, malaria involves the liver, but I don't see how creating a folder and symlinking things like malaria and alcohol would have helped.
Year 2 is a different matter. It's mostly hospital based and now medicine becomes about textbooks and your memory and experience, rather than keepnig lots of files. I don't think I would ever need to actually remember a named person's specific research findings (except for eponymous syndromes, but the original document is likely to be in German and of historical interest only). At the moment most of my Y2 notes have been handed down from various people, so I might have a file called Malaria.docx. I store this under M at the moment. I might also have files called List of liver conditions.docx or Causes of splenomegaly.docx which go under Abdominal. Again, while things like Parasitic diseases, Blood-borne diseases, Diseases involving the liver and Tropical medicine are good as tags, I'm not sure what files I would be tagging as these are actually titles of my documents. Look into MeSH if you really want to sort things this way.
My Y2 notes are not really ideal - but as I said they were mostly handed down. Also, I hate word, yes I can convert them to ODT but I have decided to convert them to HTML over the summer. I'll need these notes for the next few years and so will my girlfriend. They are entirely text files anyway, and HTML loads really fast anywhere (phone, computer room, parents' house). The advantage of this is that when Malaria appears in under Causes of splenomegaly, it can be a link to my malaria page. Also, it gives me a chance to do stuff with PHP, python, ajax, etc. if I decide to put them online (which previous students have failed to do).
When you are working hard, get up and retch every so often.