Gilles,
I've had little luck edit Hebrew (actually Yiddish) in emacs. I do all
of the editing of Lilypond except for the right-to-left markup in emacs.
Then I use gedit with great success for the Yiddish markup. It seems to
keep the directionality things right and saves properly in UTF-8. I am
using 2.6.
The main thing that I have not gotten to work are the combining
characters. Unlike Hebrew, which is technically correct without the
vowel markings, Yiddish requires the vowels. When I have tried to
include them, Lilypond places them as though they are separate
characters. They should actually be placed in the same character
location as the preceding character.