Michal, I ran into the same thing trying to replace metacity with e16. The problem is that gnome expects to find a desktop file in /usr/share/applications matching the value in desktop/gnome/session/required_components/windowmanager.. in your case it's looking for /usr/share/applications/wmaker.desktop.. and if that desktop file isn't there, it won't start your window manager, logging "WARNING: Unable to find provider 'wmaker' of required component 'windowmanager'" to ~/.xsessions-error.
Adding a wmaker.desktop file to /usr/share/applications should fix this.. if windowmaker has one in /usr/share/xsessions you can copy it over and change its "Type=Xsession" line to "Type=Application", otherwise you can copy and adapt the metacity.desktop that's already there.