I spent a little while trying to get my server to run Drupal's "clean up" cron job/tab. I tried many things from linking to the cron.php to trying to copy the clean URL that Drupal creates (/admin/reports/status/run-cron). Well, in any case, I did about 4 minutes of detective work on the Drupal website.

In order to get your cron job running (from SSH):
 
Step 1. Login to your server via SSH (Preferably not as root and as a user)
Now that you are logged in as your user, you can edit your cron tab file. This will hold all your different cron jobs.
 
Step 2. Add your job to the list! (The drupal way)
Add the following line to this file:
 
0 * * * * wget -O - -q -t 1 http://www.example.com/cron.php
 
You can substitute anything for the 0 and the stars. This will run your job at different increments! Although, i'm sure you already knew that. However, i hope this helps you get your job running!