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There is a very good feature request on Debian's BTS to add shutdown/reboot support from LTSP clients.
The reporter Vagrant gave the commands and also pointed some example code for how to do it in gnome-session.
See details: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=564264
Cheers for PCMan made a LTSP support release(0.4.4)!