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The lastest ltsp display manager (LDM above version 5.0.20) is able to use rc scripts. To set session parameters place a script with S<sequence-number>-<descriptive name> in /opt/ltsp/i386/usr/share/ldm/rc.d/ and it will get executed in the users session during login:

as an example lets have a look at the /opt/ltsp/i386/usr/share/ldm/rc.d/S15-screensaver-blankonly script

#
# sourced with .
#
# Script to automatically switch gnome screensaver to blank only mode
#
ssh -S ${LDM_SOCKET} ${LDM_SERVER} "/usr/bin/gconftool-2 --set --type string /apps/gnome-screensaver/mode blank-only"

if the ssh tunnel is established (during login after the password was verified), the script will ssh into the session (done by the "ssh -S ${LDM_SOCKET} ${LDM_SERVER}" prefix) and will execute the command in quotes.