I was using xmodmap ~/.Xmodmap in my .Xsession to remap caps lock to the super key utilizing the following configuration in .Xmodmap:

! disable caps lock and map to super
clear Lock
remove lock = Caps_Lock
add mod4 = Caps_Lock

After some updates in Debian testing, this configuration did not work anymore. I found some information on http://lists.debian.org/debian-x/2011/04/msg00291.html.

After reading /usr/share/X11/xkb/rules/base.lst, a working way seems to be using setxkbmap with the option caps:super:

setxkbmap -option caps:super

At the moment I am too lazy to read the documentation on XKB, so I am using xmodmap for the remaining keymappings. The right way should involve some configuration files documented on http://madduck.net/docs/extending-xkb/ and http://www.charvolant.org/~doug/xkb/

An introduction to the evolution of X.org can be found on http://wiki.debian.org/XStrikeForce/InputHotplugGuide