I'm using emacs-snapshot-gtk, and the locale of mine is en_US.UTF-8.
By setting GTK_IM_MODULE=SCIM (I also tested XIM) and XMODIFIERS="@im=SCIM", scim works well on all gtk applications. But scim cannot be actived on emacs-snapshot-gtk no matter how I configure language environment in dot emacs file.
But, if I login in Failsafe xterm session of GDM, that is, the simplest X session with only xterm started. Then I started scim daemon and configured all environment variables needed, such as XMODIFIERS, scim can be used on emacs-snapshot-gtk, however. As soon as gnome-settings-daemon is started, scim cannot work on emacs-snapshot-gtk any more.
I also tested emacs-snapshot and emacs21, the same results are obtained. So it seems that gnome-settings-daemon prevent scim working on emacs, including emacs-snapshot and emacs21.
By the way, a very strange thing is, scim can work on emacs on my laptop, which runs also Debian Sid on it. I don't know why