http://ffmpeg.org/

Converting FLAC to AAC in an MPEG4 container:

ffmpeg -i in_filename.flac -acodec libfaac -ab 384k out_filename.m4a

Converting anything in an AVI container (that you have a decoder for) to MPEG2 for DVD-Video. Dual Pass.

#!/bin/bash

if [ ! "$1" ]
then
	echo "No filename provided"
	exit 1
fi
if [ "${1/.avi/.mpeg}" = "$1" ]
then
	echo "Only .avi files supported"
	exit 1
fi


MENC=`which mencoder`

OPTIONS="\
	-quiet \
	-of mpeg \
	-ofps 25 \
	-mpegopts format=dvd:tsaf \
	-oac lavc \
	-ovc lavc \
	-srate 48000 \
	-af lavcresample=48000 \
	-vf scale=720:576,harddup \
	-lavcopts aspect=16/9,acodec=ac3:\
abitrate=192:vcodec=mpeg2video:vrc_buf_size=1835:\
vrc_maxrate=9800:vbitrate=8000:keyint=15:precmp=2:\
subcmp=2:cmp=2:dia=-10:predia=-10:cbp:mv0:vqmin=1:\
lmin=1:dc=10:vstrict=0:trell:mbd=2"

OPTIONS_1="${OPTIONS}:vpass=1"
OPTIONS_2="${OPTIONS}:vpass=2"

echo 1st Pass
$MENC $OPTIONS_1 -o /dev/null $1 

echo 2nd Pass
$MENC $OPTIONS_2 -o "${1/.avi/.mpeg}" "$1"