I've noticed that wmaker puts WPrefs in /usr/share/GNUstep/WPrefs.app/WPrefs, which is against the FHS requirement that /usr/share be arch-independant files only. I don't pretend to have a good fix for this, but I figured at least I'd bring it up, suggest alternatives, and let someone else have the fun of deciding what, if anything, to do about it. The FHS was written without consideration to self-contained application packages such as those used by GNUstep and ROX. There isn't really any suitable place for them in the FHS, however Debian breaks WPrefs out of its .app directory and throws the various files all over the filesystem. I don't like this non-solution. NeXT used /Applications for these things, but that also would not make sense on a non-NeXT UNIX-based system since that thinking is contrary to the way many or most systems are laid out in terms of partitions. /usr/GNUstep/Applications might work, though obviously any such thing is also against the letter of the FHS. I think providing /usr/GNUstep/Applications/WPrefs.app/Wprefs -> /usr/bin/WPrefs is probably sufficient to satisfy its intent in a round-about manner, however.
Fixed now. Moved to /usr/lib/GNUstep which is less stupid and doesn't violate FHS.