With regards to the servers' physical resources, monitoring the amount of free memory and disk space is recommended, as consumption of these can be substantial depending on types and numbers of analyses being run.
Monitoring metrics of the CLC Server itself enables you to keep tabs on how well the jobs processing is going. The metrics the CLC Server provides are available as JMX20.1 attributes. Software from a third party will be necessary to set up the monitoring of these attributes. Numerous software products for this are available and most support JMX. If your monitoring software supports the raising of alarms, you can set up triggers based on these metrics to receive alerts when a situation arises that needs attention.