Can anyone recommend any apps or software to store/organise all my journal articles, photocopies and scanned in copies of notebook pages which are currently stored in a very hideous-manner!

Ideally I want something where I can add tags to a document when I add it, so that, for example, I can search keywords and come up with all the relevant papers and notes when writing later.

Mendeley - just convert everything to a pdf and it's great. Search option is great too.

I'd second Mendeley. You can make notes in it too, and highlight text etc.Plus you can exclude unpublished material (your own notes for example), and its also a reference management software,

I'll third Mendeley. All the above, plus it's free.

Mendeley is really great and very easy to use.