It's really hard to judge which games have the most players, Microsoft and Sony don't seem to fond of sharing stats, but PC sites like Steam give a pretty comprehensive list showing the number of servers and players.
As of today Dota 2 had the most players peaking at around 865,000 followed by Counterstrike at nearly 245,000.
This doesn't account for console gaming though or non-Steam games such as League of Legends and World of Warcraft, which were previously known as the most popular online games.
This article shows how controversial it can be to name one game as the most popular and by the looks of things League of Legends is still more popular than Dota 2, because of it's eastern fan base: