Following are the best practices:
Use SSL certificates wherever applicable, and set the time zone of each of the vRealize Operations Manager nodes correctly. The Nodes will not communicate with each other if they are out of sync with the time.
Monitor resources and utilizations of VDCs as well as virtual machines. Ensure that you set correct threshold values and alert notifications for the same.
Create custom thresholds based on your applications' needs. Leverage vRealize Hyperic to monitor your applications, such as SQL Databases, MS Exchange, Oracle, and so on.