I have domain1.com hosted as the primary domain with domain2.com "parked" at domain1.com. My public_html/sites folder looks like this:
My webhost (an Apache server running Cpanel 11) blocks user access to lynx or wget, so the normal recommendations for setting up a crontab were not working for me. However, I discovered a suggestion in http://drupal.org/cron to try the cron-curl.sh script that ships with Drupal in the "scripts" folder. I edited cron-curl.sh so that it includes the following line:
curl --silent --compressed http://domain1.com/cron.php
And then I set up a crontab that looks like this:
*/2 * * * * /home/webhostaccountname/public_html/scripts/cron-curl.sh
After remembering to set the file permissions on cron-curl.sh so that it could be executed, the cron job worked perfectly. The "*/2" executes the crontab every other minute for testing purposes only.
So, then I went back into cron-curl.sh and added the following line:
curl --silent --compressed http://domain2.com/cron.php
Again, success! I'm watching the logs for both domain1.com and domain2.com. Cron jobs are being executed every 2 minutes for both domains.