Networking has always been a more or less imperfect science…perhaps more of an art? The TCP/IP suite of protocols are designed with the base concept that transmitting packets of data is prone to errors and the protocols need to have mechanisms built in to manage dropped packets, latency, and other issues.
With normal data networking it may not be a big deal if packets arrive out of order. As long as the TCP/IP protocols can reassemble them in the proper order there may be a millisecond or two of lag but the data will get there. However, with voice and video a millisecond may as well be a millenia. With VoIP, and audio/video conferencing it is much more important that data arrive quickly and in order.
Microsoft provides a comprehensive amount of guidance and documentation including Troubleshooting Enterprise Voice: Approaches, Procedures, and Tools.
One valuable tool for monitoring and troubleshooting network issues is a network analyzer (also known as a protocol analyzer or packet sniffer). I recently had an opportunity to work with the Capsa Enterprise Network Analyzer and would recommend it as a powerful, cost-effective tool for troubleshooting VoIP / UC, as well as other network issues. You can learn more about Capsa Enterprise from this review (there is also a link to a more extensive product white paper).