HighMem

Derived from [1], but a little bit better:

#!/bin/bash
# usage: $1: cue file, $2: audio file (e.g. .ape) $3: format (e.g. flac)
shnsplit -f $1 -o $3 -t %n-%t $2
for i in *.$3; do mv "$i" "`echo $i | sed -e 's/ /_/g'`"; done
cuetag $1 *.$3

[1]http://aidanjm.wordpress.com/2007/02/15/split-lossless-audio-ape-flac-wv-wav-by-cue-file/