I wondered about the same thing a while ago... The best solution I could find is a plugin for audacious from gentoo-china overlay.
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layman -a gentoo-china
emerge -av audacious-mac
This will also pull commandline tool for ape files (the ebuild is called mac-port but the program itself is just 'mac' IIRC)
I've also heard about a gstreamer plugin for APE codec, but I never tried it.
Also you might want to consider converting your APE files to a more linux-friendly format, e.g. flac or wavpack (I recon both of them can be played with amarok). You won't loose any quality with this feat - they are all lossless after all
. For that purpose you can for example convert APE files to plain WAVs with that 'mac' tool, which you can then encode to flac or wavpack.