Media Converter

gnormalize [My Pick!] for Linux
gnormalize is an audio converter, a front end to normalize, an encoder/decoder, a ripper, a metadata (tag) editor and a audio player. It uses gtk2-perl under GNU/Linux.
gnormalize.sourceforge.net

foobar2000 (for Windows)
APE -> MP3
http://www.foobar2000.org/
Download foobar2000 and install it.
Download Monkey's Audio decoding support for foobar2000 from http://www.foobar2000.org/components/index.html
Install Monkey's Audio decoding support for foobar2000.
Download LAME for Windows and install it.
http://www.softpedia.com/progDownload/LAME-MP3-Encoder-Download-6952.html
Set converter configuration in foobar2000: File > Preferences > Tools > Converter > Encoding Presets > Add New > Encoder: MP3 (LAME) Quality: Best quality and check the Fast mode.
Open .cue sheet file and start convert.
Note: File name in the 3rd line of .cue file must as same as the .ape file's name.