eac3to is able to convert E-AC3 and TrueHD audio tracks to AC3 or FLAC.

Usage: eac3to src.eac3|evo|wav dst.ac3|flac|raw|wav [-options]

This tool can convert a 2.0 or 5.1 E-AC3 or a 5.1 TrueHD track to AC3/FLAC.

Features:

• can show information about audio, video and VOB/EVO/(M2)TS files
• can decode and encode various audio formats
• can remove dialog normalization from AC3, E-AC3, DTS and TrueHD tracks
• can extract AC3 stream from Blu-Ray TrueHD/AC3 tracks
• can extract TrueHD stream from Blu-Ray TrueHD/AC3 tracks
• can extract DTS core from DTS-HD tracks
• can remove DTS zero padding and repair outdated DTS-ES headers
• can apply positive or negative audio delays
• can reduce bitdepth of decoded audio data by using TPDF dithering
• can resample decoded audio data (using "r8brain")
• can apply/reverse PAL speedup on decoded audio data (using "r8brain")
• can demux all video and audio tracks of an EVO/VOB/(M2)TS source file
• can join/rebuild multiple EVO/VOB files
• can remux the video track of a EVO/VOB/(M2)TS source to Matroska

eac3to sourcefile[+sourcefile2] [trackno:] [destfile|stdout] [-options]

Examples:

• eac3to source.pcm destination.flac
• eac3to source.thd destination.flac destination.ac3
• eac3to source.evo 2: destination.eac3 3: destination.flac
• eac3to feature_1.evo+feature_2.evo movie.mkv
• eac3to 00001.m2ts movie.mkv

If you prefer a graphical user interface, here´s a GUI made by The_Keymaker:

http://madshi.net/EAC3toGUI.zip

What's New in version 2.66:

• changed eac3to to allow AAC encoding with 7.1 channels (for new Nero encoder)
• fixed AGM creation for files bigger than 4GB
• added support for Nero's new AAC Encoder download URL
• lowered volume of error/success sounds
• when there are 2 similar playlists the one with less chapters is ignored now