I have an extensive audio selection on my harddrives. It must remain oranized due to it's size (it's one of my things). Tag&Rename (30$) is what I use to manage my collection. It is very good at organizing my new music into the style I want them renamed and saved in. You can setup quick buttons that rename the files/folders into exactly the format you want. I've organized my collection by Artist/Year Album (bit rate)/track – title.flac. It also allow quick playlist generation and embed album art.
I really like how it will edit every tag in every standard. The only thing missing is lyric grabbing. For that I use MiniLyrics. It's not perfect but it does save the files to the album's folder as well as embed the lyrics in the files themselves.