This includes at least gnome-panel, xfce4-panel, fbpanel, and a few other commonly used panels.
I've managed to fix these problems in all of the above and likely many others by adding a simple raise(); before giveInputFocus(); on pekwm/src/Frame.cc at line #2055.
It seems most if not all taskbars assume sending a NET_ACTIVE_WINDOW atom is enough to give input focus _and_ raise the window.
I haven't noticed anything being broken by my quick hack, your mileage may vary.
Added a raise before the giveInputFocus.
The standard does not, as far as I can see, mention anything about how the window is to be activated just that it is to be, but input focus on a window below all other windows does not make sense.