I personally use a music tagging/renaming program called Picard. Point it at a relatively unorganized music folder, it tries to identify each track based on the existing metadata or acoustic signature, adds/modifies the track metadata based on the Music Brainz database, and runs a custom renaming script that moves it into place per my preferences.

Its not as automated as I would like, and takes some hand holding, but keeps my collection clean and standardized.