MediaCoder can use MPlayer, Winamp input plugins or Lame as audio decoder (it decodes audio from both audio files or video files) and encode to various formats by pushing audio samples to various encoder backends.
Hardware Environment:
* CPU: Intel Core2 E6300 @ 2.1Ghz
* Motherboard: Gigabyte GA965P
* Memory: 1G DDR2 667 x 2
* Hard Drive: Western Digital Caviar SE16 KS 250G (SATA2)
* Display Adapter: GeForce 7300GT
The original file format is FLAC 44.1KHz/Stereo @948Kbps.
CODE
Encoding Speed
(playtime 1x) Target Format
------------------------------------------------------------------------------------
119.0x IMA ADPCM / FFmpeg
64.8x MP3 / HelixMP3
54.3x WavPack (Best Compression) / WavPack Compressor (@929 Kbps)
47.6x MPEG-4 ALS / ALS Reference Codec (@940kbps)
42.0x AC-3 / FFmpeg
40.6x HE-AAC v2 / Nero 1.1.34.2
38.3x WMA 9 / Windows Media Format SDK
34.6x WMA 8 / FFmpeg
34.3x HE-AAC v2 / CT AAC+ Encoder
33.6x WMA 7 / FFmpeg
32.9x HE-AAC / CT AAC+ Encoder
31.3x Speex / Speex Encoder (44.1khz->16khz on-the-fly resampler applied)
31.0x LC-AAC / CT AAC+ Encoder
28.0x FLAC (Compression = 8)/ FLAC Encoder (@948kbps)
24.5x HE-AAC / Nero 1.1.34.2
24.4x MusePack / MPC Encoder
23.6x Vorbis / OggEnc 2.83 Lancer SSE3
23.6x Vorbis / OggEnc 2.83 Lancer SSE2
23.5x Vorbis / OggEnc 2.83 Lancer SSE
23.2x LC-AAC / Nero 1.1.34.2
22.4x APE (Extra High) / Monkey's Audio (@906kbps)
20.1x MP3 / LAME 3.98a5
18.5x Speex / Speex Encoder (44.1khz->32khz on-the-fly resampler applied)
17.5x LC-AAC / FAAC 1.25
16.3x Vorbis / OggEnc 2.84 aoTuVb5
15.4x Vorbis / OggEnc 2.84 original
(playtime 1x) Target Format
------------------------------------------------------------------------------------
119.0x IMA ADPCM / FFmpeg
64.8x MP3 / HelixMP3
54.3x WavPack (Best Compression) / WavPack Compressor (@929 Kbps)
47.6x MPEG-4 ALS / ALS Reference Codec (@940kbps)
42.0x AC-3 / FFmpeg
40.6x HE-AAC v2 / Nero 1.1.34.2
38.3x WMA 9 / Windows Media Format SDK
34.6x WMA 8 / FFmpeg
34.3x HE-AAC v2 / CT AAC+ Encoder
33.6x WMA 7 / FFmpeg
32.9x HE-AAC / CT AAC+ Encoder
31.3x Speex / Speex Encoder (44.1khz->16khz on-the-fly resampler applied)
31.0x LC-AAC / CT AAC+ Encoder
28.0x FLAC (Compression = 8)/ FLAC Encoder (@948kbps)
24.5x HE-AAC / Nero 1.1.34.2
24.4x MusePack / MPC Encoder
23.6x Vorbis / OggEnc 2.83 Lancer SSE3
23.6x Vorbis / OggEnc 2.83 Lancer SSE2
23.5x Vorbis / OggEnc 2.83 Lancer SSE
23.2x LC-AAC / Nero 1.1.34.2
22.4x APE (Extra High) / Monkey's Audio (@906kbps)
20.1x MP3 / LAME 3.98a5
18.5x Speex / Speex Encoder (44.1khz->32khz on-the-fly resampler applied)
17.5x LC-AAC / FAAC 1.25
16.3x Vorbis / OggEnc 2.84 aoTuVb5
15.4x Vorbis / OggEnc 2.84 original
* MediaCoder uses separate processes for decoding and encoding audio which makes dual-core processors a little better utilized.
MediaCoder (including the Audio Edition) can be freely downloaded here. You can also transcode audio track from most popular video formats directly with MediaCoder.

EDIT1: modify Speex benchmark, add original OggEnc benchmark and sort the results
EDIT2: add final bitrate info for lossless encoding
