Paloma is a program to manage an SQL database of digital music files, and facilitate their retrieval and playback in interesting ways. It works with music files of any form -- MP3, Ogg Vorbis, MIDI... whatever you've got a player for. Paloma makes it easy to rip your entire CD collection and store it on your hard disk (or a collection of CD-Rs) for instant random access; playlists can then be generated using arbitrary SQL commands.
SoX is the Swiss Army knife of sound processing tools: it can convert sound files between many different file formats and audio devices, and can apply many sound effects and transformations, as well as doing basic analysis and providing input to more capable analysis and plotting tools.
mp3clean takes a list of files and presents each file's ID3 tag for re-editing. If no ID3 tag is found, mp3clean will go through great effort to clean up and create a suggestion for ID3 tags from looking at the filenames. When you are satisfied with the ID3 tags, mp3clean will create a nice filename from the ID3 tag, based on your format string and general cleanup rules.
Lava's jWave is a versatile set of packages for Java that allow you to easily create and process RIFF files, with a special emphasis on reading and writing Microsoft PCM .wav files. jWave was initially released as an integrated feature of Lava, a general-purpose class library for Java. By popular demand, it is distributed in its own bundle.