Well, transparent proxy is a way to "force" computer clients to use the proxy of the server.
How?
* Mainly some tweaking of the firewall rules to redirect port 80 traffic -> 3128 and a little modification in SQUID
Why?
* It reduces client configuration (you dont need to configure each client's navigator, actually with DHCP you would just need to configure email manually)
* It forces to the usage of the proxy for web traffic. This could be related to many other features (QoS, some kind of content filtering, antivirus, etc)
Any bad point?
* It needs a faster server machine.
* You loose some characteristics of SQUID, mainly the possibility to control the usage by user / IP (now for the proxy all traffic comes from the same IP, the server itself)
About the last comment, I dont know if it comes standard in 5.1.2 but sure there is a howto around.
Hope it helps.