Yep. Years ago I settled on a convention of always installing a virtualenv into a 've' directory in the project so I can just set the shebang line on scripts (eg, django's manage.py) to "#!ve/bin/python". My Django project template sets all that up for me automatically. So now I just have muscle memory for typing "./manage.py ..." etc and I never have to activate virtualenvs, mess around with virtualenvwrapper type hacks or accidently run one project's script with a different project's virtualenv activated.
* bash command line
* cron
* or daemon manager like supervisord