There are two little applications that are often missed by new system administrators and/or desktop users and these are cron and at. These little critters can make your life easy when running resource intensive tasks that can wait until everyone is no longer using the system or when the demand for CPU resource is low.
When you need to run a task or two regularly, at set intervals, you use cron. When you need to run a task at a specific time, you use at. To better understand it (so you can maximize its power), here's a Linux tip from IBM's Ian Shields.
So, when you need to empty the cache regularly at quarter-past two in the morning, no need to wake up, remotely login and do it yourself – just let cron do the job. :)