Now processing of Ice messages has been added to the main event loop so it is now also possible to properly shut down the session running, this has been tested with Gnome 2.26.1 (Ubuntu Jaunty), closing the issue.
Could you please try again with git head, still pekwm does not detect the session is being ended though.
Update: This does not seem to work any longer with Gnome 2.26 :/
03:04:00For now you can use PekWM in Gnome by editing the windowmanager value in Gconf:
open gconf-editor and go to /desktop/gnome/session/required_components and change the value of "windowmanager" from metacity to pekwm.
Then you need to create a desktop entry for PekWM in /usr/share/applications (or wherever your distro puts your .desktop files).
Restarting the session should bring up a Gnome + PekWM session.
Of course this is not a really elegant solution, since it doesn't allow replacing PekWM with another WM, without killing it (i.e. the "--replace" flag you find in WMs like Metacity won't work).
Pekdon mentioned that he's working on it, so stay tuned. :)
Ryos pointed out on irc that this related to http://bugzilla.gnome.org/show_bug.cgi?id=555406
A friend mentioned to me that nautilus may have acquired the root window. Please try to quit metacity and nautilus before starting pekwm.