So after letting the auto tagger run all last night I now have my collection of music in a decent state. Next is the cleaning up of the collection. To do that I went and downloaded Media Library Organiser plugin. This great plugin renames files, builds a neat folder structure and removes duplicates. You can specify what the structure is (by default [Artist]\[Album]\[Track No] [Title].[File Extension]) and you can turn on/off the duplicate removal etc... Since this is all tagged base you desperately need to make sure your tags are done right first. This takes just a few minutes for thousands of audio files to be cleaned up.