Following server maintenance at 18:00 PDT on August 27, Blizzard has changed the way Realm population is displayed, making it more intuitive. A large section of the playerbase have complained about long queue times on their Medium population servers, stating that the system is counter-intuitive. Here's how the old system worked.
Old System
The system used to calculate each server's population by comparing them to the most populated server. By doing this, highly populated realms (with long queues) were shown to have a Medium population when compared to the most populated realm in the region (which had an even longer queue).
New System
The current system calculates each server's population relative to the maximum number of players that server can support. This way, a Medium population server is indicative of a reasonable population (which is still higher than it would have been in 2006), and lets players connect without having to deal with queues. High population now represents a server which is close to having a queue, and players trying to connect to a Full server will have to face queues.