Some awesome Emacs Lisp programs that relies on external programs:
mu4e: http://www.djcbsoftware.nl/code/mu/mu4e.html
not much: http://notmuchmail.org/
EDBI: https://github.com/kiwanami/emacs-edbi
ropemacs: http://rope.sourceforge.net/ropemacs.html
RSense: http://cx4a.org/software/rsense/index.html
GCCSense: http://cx4a.org/software/gccsense/index.html
emacs-ipython-notebook: http://tkf.github.io/emacs-ipython-notebook
emacs-jedi: http://tkf.github.io/emacs-jedi
request.el: http://tkf.github.io/emacs-request/
Well, the last three is my projects so you could exclude that :)
Also, we could add version conrolling interfaces such as magit and VC (relying on git/svn/hg/...) and advanced interpreter such as SLIME/nrepl.el/geiser.
Ah, and don't forget dired!
And then again, they are pain in the arse (if not impossible) to use on Windows. One of the benefits of ELisp extensions is that they are multiplatform.
I agree some of them are harder to setup in Windows. But it helps (or forces) developers to make these tools and languages cross-platform, which is good, I think. And I guess making them cross-platform is actually easier than implementing them purely in Emacs Lisp.
It does fill a need or 3, I must admit, and I hate to be negative, but if that is the best example you can come up with of the positive effects of putting Emacs functionality in external programs, that makes me lean towards the conclusion that it is a bad idea to put Emacs functionality in external programs!