mac file.ape file.wav -d
cuebreakpoints file.cue | shnsplit file.wav && rm file.wav

На выходе порезанные wav'ы. На кой здесь нужны программы с окошками, не понятно ни разу.

P.S. ape2ogg.sh:
=========================
#!/bin/sh
mac "$1" "${1%ape}wav" -d
cuebreakpoints "${1%ape}cue" | shnsplit "${1%ape}wav" && rm "${1%ape}wav"
oggenc -q 7 split-track*wav && rm split-track*wav
cuetag.sh "${1%ape}cue" split-track*ogg
=========================

Чем это лучше cue2tracks?

Specifying quality rather than bitrate (to a very high quality mode)
oggenc infile.wav -q 6 out.ogg
(Режим с указанием качества предпочтителен)
Specifying a high-quality encoding averaging 256 kbps (but still VBR).
oggenc infile.wav -b 256 out.ogg
Adding some info about the track:
oggenc somefile.wav -t "The track title" -a "artist who performed this" -l "name of album" -c "OTHERFIELD=contents of some other field not explicitly supported"

Fixed bit rate jstereo 128 kbps encoding, highest quality (recommended):
lame -h sample.wav sample.mp3
Variable bitrate (use -V n to adjust quality/filesize):
lame -h -V 6 sample.wav sample.mp3
(тооже предпочтительно)
Fixed bit rate jstereo 112 kbps encoding:
lame -b 112 sample.wav sample.mp3