Digital Audio File Formats

PCM

Wave File (.wav)

Originally a Windows-based file type; virtually all software on all platforms can use them now.
Used to save waveform data in a variety of bit resolutions (both fixed and floating-point), sample rates and channels of audio.
Wave files can be split or interleaved.
Data is stored in chunks.
All serious audio should use linear PCM coding, although wavs also supports psychoacoustic wordlength reduction.

Broadcast Wave (.wav)

As above, but with a broadcast wave extension added by the EBU. This includes all essential broadcast info such as unique source identifiers, station etc.
BWF cannot handle linear PCM multichannel data at present.

Audio Interchange File Format (.aiff)

Commonly used on Macs.
Up to 32 bit fixed-point resolution, with sample rate support up to 192 kHz.
AIFF files can be split or interleaved.
Data is stored in chunks.

Sound Designer Ⅱ (SDⅡ) (.snd)

Developed by Digidesign for their now defunct Sound Designer stereo editor.
Commonly used in media production on Macs, although it is rumoured that the file type has been obsoleted by Digidesign…
A nightmare on PCs, due to it's reliance on resource and data forks.

DSD

There is currently a bun-fight between two sides of the audio world about what will replace CD. One side is covered by DVD-A, a 24-bit 96 kHz surround-ready PCM format. On the other side is SACD, another surround-ready format which uses DSD (Direct Stream Digital). DSD uses a bitstream which has a bit resolution of 1, and a sample rate of 2.822 MHz (64 times that of CD). Which is best? Does the consumer care? We'll have to wait and see …

Metafile Formats

Metafile formats are an attempt to get all audio software manufacturers to play nicely, providing a single file type which all software can use. Unfortunately, manufacturers don't think this way most of the time…

AES-31

A file type by the AES (Audio Engineering Society) to interchange basic projects, with timestamping and crossfade information. Have a look at the specification PDF.

OMF (Open Media Format)

This is a Digidesign format to exchange Pro Tools sessions with other workstations. Support is a bit flaky at the moment, but Logic's implementation is good.

Psychoacoustic Wordlength Reduction

Psychoacoustic wordlength reduction is the process of reducing the size of a file by sacrificing some audio data which is thought to be either inaudible or unimportant. These codecs are 'lossy', meaning that once sound has been encoded it has lost elements which cannot be restored. Also, don't believe manufacturers who say that these files are CD quality!

Loud noises can mask sounds that are both lower in level and relatively close to the louder signal's frequency.
Perceptual coding schemes (such as ATRAC, MP3, WMA and AAC) filter out the sounds that (supposedly) can't be heard.
'Lossy' or 'destructive' process; the data can't be replaced once filtered out.

ISO-MPEG Audio Layer 3 (MP3) (.mp3)

Stands for Moving Picture Experts Group.
Developed by the Fraunhofer Institute and Thompson Multimedia.
Compresses digital audio by factors of 10:1 and greater with near-CD quality.
Not all MP3 codecs are of equal quality; some (e.g. the Fraunhofer codec at 160 kbps) sound great, while some are noticeably inferior.

ATRAC

ATRAC (Adaptive Transform Acoustic Coding) is the compression codec used in minidisc.

Window Media Audio (WMA)

Developed by Microsoft for the Windows Media Player.
Allows for data compression.
The current standard-bearer is WM9.

Advanced Audio Coding (AAC) AKA MPEG 4

Surround-compatible format with high-quality data reduction.
Capable of encoding up to 48 channels at 24/96 in a single bitstream.
SDMI (Secure Digital Music Initiative) compatible; this is the format Apple have built into Quicktime and used for their innovative legal music downloading service.

Ogg Vorbis

Possibly the best name ever for a file format!
An open-source alternative to MP3 and AAC; developed by Xiph and now developed by the music community.
Very good subjective performance due to variable bit rate encoding. Have a listen at this comparison page and see how it stacks up against MP3, MP4, AAC, Real Audio, WMA and others.
Not developed for profit (unlike MP3) but for the audio community.
Not widely supported (yet), so if you like it, use it and help make a free, open-source, high-quality standard!

An additional file type is the lossless encoded file; Apple Lossless and Windows Media Audio 9 Lossless are two of many.