MediaMonkey is what I used to use back when my music was a mess, and it did a rather good job of cleaning it up for me into a file structure I liked. But Winamp is the best music player I've ever used, and I would be surprised if I found one I liked better.
EDIT: Also, I use Tag&Rename for all my tagging after ripping with EAC - actually, that program can handle managing file structures pretty well, but I don't know if it could clean up multiple locations/drives all in one go like MediaMonkey might be able to.
for mass tagging. Don't be misleaded by the name it supports formats from AAC to WavPack. Haven't come across a better one yet.
Media Player Classic Home Cinema and VLC for single file playing and video.
Winamp for playlists.