I found all the suggestions had the "multiple open-ended" approach style of Windows. Monchant's piece on OneNote - at least, gave me an idea of a tool that seems could be useful for referencing.
To be honest, I am worn out using the resident Windows file folder system as a storage system. There are huge overheads.
But I keep on telling my students - it is the only place to readily available to them. Although it is crucially inadequate as their files aren't exposed over the Net.
I think a remote storage system with strong organisation and cross-referencing abilities would be a better solution in the long run.
Any ideas ?