wmakerconf is a gtk program whereas the WPrefs.app is written using the native wmaker WINGs library. wmakerconf includes the same configuration possibilities as WPrefs.app -except for anything new which has been added to wmaker the last couple of years(one option I know: single-click launching of DockApps).
For configuration files and extras, you may want to have a look at my src2pkg build scripts and Resources here:
http://distro.ibiblio.org/pub/linux/...wmaker-0.92.0/
I have not updated the build there, but the conf files, etc are still the same.
Besides the DockApp area linked to above, you'll find more wmaker-related stuff here:
http://distro.ibiblio.org/pub/linux/...s/WindowMaker/