Cron job is a server side setting for periodically executing scheduled tasks on your server. It is useful for example for clearing logs, sending periodical reports, saving dummy recurring commissions and many other things.
It is also very useful to process the visits, clicks, transactions in an offline manner. This way you can avoid high server load and process a lot more transactions compared to online/real time processing.
If you want to be able to run periodic tasks, such as sending daily, weekly or monthly reports by e-mail automatically or generate recurring commissions, then you should configure a cron job to be executed every X minutes (X = 1, ... ,15). Ideal setting is below 5 minutes.
More info about setting up can be found in the merchant panel at Tools > Integration > Cron job integration
If cron job is not running, the system will track the affiliate-referred clicks, sales/leads, but the above mentioned periodical features will not work.