Tengo la impresión de que el uso del distintivo --system-site-packages con virtualenv permitirá que el entorno virtual utilice los paquetes del sistema ya instalados. Sin embargo estoy encontrando que este no es el caso. Estoy usando una versión compilada personalizada de python. Puedes ver el problema en los pasos a continuación.

[user@machine django]$ which python
/app/python/bin/python
[user@machine django]$ which pip
/app/python/bin/pip
[user@machine django]$ which virtualenv
/app/python/bin/virtualenv
[user@machine django]$ python
Python 2.7.3 (default, Jul 27 2012, 11:30:41)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import django
>>> exit()
[user@machine django]$ pip freeze
Django==1.4.2
distribute==0.6.30
mercurial==2.3.2
python-ldap==2.4.10
virtualenv==1.8.2
wsgiref==0.1.2
[user@machine django]$ pip --version
pip 1.2.1 from /app/python/lib/python2.7/site-packages (python 2.7)
[user@machine django]$ env
<snip>
LD_LIBRARY_PATH=/app/python/lib:/app/openldap/lib:/app/instantclient_11_2
PATH=/app/python/bin:/app/openldap/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bin/cfdelivered:/home/user/bin:/app/oracle/product/java/jdk1.6.0_30/bin
PYTHONPATH=/app/python/lib/python2.7
[user@machine django]$ virtualenv --system-site-packages --distribute --python /app/python/bin/python2.7 foo
Running virtualenv with interpreter /app/python/bin/python2.7
New python executable in foo/bin/python2.7
Also creating executable in foo/bin/python
Installing distribute...<snip>...done.
Installing pip................done.
[user@machine django]$ . foo/bin/activate
(foo)[user@machine django]$ which python
/app/xxx/django/foo/bin/python
(foo)[user@machine django]$ which pip
/app/xxx/django/foo/bin/pip
(foo)[user@machine django]$ env
<snip>
LD_LIBRARY_PATH=/app/python/lib:/app/openldap/lib:/app/instantclient_11_2
VIRTUAL_ENV=/app/xxx/django/foo
PATH=/app/xxx/django/foo/bin:/app/python/bin:/app/openldap/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bin/cfdelivered:/home/user/bin:/app/oracle/product/java/jdk1.6.0_30/bin
PYTHONPATH=/app/python/lib/python2.7
(foo)[user@machine django]$ python
Python 2.7.3 (default, Jul 27 2012, 11:30:41)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import django
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named django
>>>

Resultados de python2.7 -c "import sys; print (sys.path)"

Normal:

[user@machine django]$ python2.7 -c "import sys;print(sys.path)" ['', '/app/python/lib/python2.7/site-packages/cx_Oracle-5.1.2-py2.7-linux-x86_64.egg'‌​, '/app/python/lib/python2.7/site-packages/python_ldap-2.4.10-py2.7-linux-x86_64.e‌​gg', '/app/python/lib/python2.7', '/app/python/lib/python27.zip', '/app/python/lib/python2.7/plat-linux2', '/app/python/lib/python2.7/lib-tk', '/app/python/lib/python2.7/lib-old', '/app/python/lib/python2.7/lib-dynload', '/app/python/lib/python2.7/site-packages']

Dentro de venv:

(foo)[user@machine django]$ python2.7 -c "import sys;print(sys.path)" ['', '/app/xxx/django/foo/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg', '/app/xxx/django/foo/lib/python2.7/site-packages/pip-1.2.1-py2.7.egg', '/app/python/lib/python2.7', '/app/xxx/django/foo/lib/python27.zip', '/app/xxx/django/foo/lib/python2.7', '/app/xxx/django/foo/lib/python2.7/plat-linux2', '/app/xxx/django/foo/lib/python2.7/lib-tk', '/app/xxx/django/foo/lib/python2.7/lib-old', '/app/xxx/django/foo/lib/python2.7/lib-dynload', '/app/xxx/django/foo/lib/python2.7/site-packages']