The new X Server doesn’t like to play nice with other daemons. Starting X with a running moused pretty much ensures a not working mouse, if you’ve still some mouse input configuration in xorg.conf. So, having a mouse configured via xorg.conf and not using moused works fine, as long as the following Option is set in the ServerFlags section:

Option “AllowEmtpyInput” “false”

Another way for me to get the mouse working was to delete all the input configurations, a started moused and the above option. Unfortunately, you have to configure the input devices via hald, which wasn’t working for me at all.