I guess that depends on how you decide to define 'popular' and game. As Instgtr says, WoW is the most popular paid-mmo, but there plenty of other games that get played A LOT more than WoW. For example, there are literally tens- or hundreds- of thousands of Star Craft and CounterStrike games being played at any one instant.
There are also social networking games that have online player counts that dwarf almost all paid-MMOs together. For some strange reason, farming seems to be one of the more popular games in almost any country. In fact, on a recent trip to China I noticed people playing what looked to be a strange variant of the farming game instead of working! What a job that must be! lol...anyhow.
I guess it all comes down to your definition. So, does genre count? Is pay to play a requirement?