Transparent clocks are used to route timing messages within a network. A transparent clock (often this is a PTP enabled switch) allows you to timestamp the packet before it reaches a slave device, allowing for the delay to be more accurately calculated. They operate in place of a normal switch, which can otherwise introduce inaccuracy when the network gets congested.
Transparent clocks also help manage the ordering of packets if they are coming from multiple sources. If the output port is busy it will queue packets, then stamp each packet with an arrival and departure time to account for the time it was waiting in the clock.
Used when: Ethernet timing must pass through switches.