There is no "Open with" for ECMerge in Nautilus (GTK file browser). How can I integrate ECMerge with it?

You can run an Open with script from Nautilus by executing this in your user account:

echo ecmerge \"\$@\" > ~/.gnome2/nautilus-scripts/Open\ with\ ECMerge
chmod +x ~/.gnome2/nautilus-scripts/Open\ with\ ECMerge

It will add an "Open with ECMerge" menu item under the mouse Right Click/Scripts menu.