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!