Over 16 million people watered their FarmVille crops yesterday. While AppData’s Facebook app top 10 is mostly populated by games like Zynga’s popular farming game, Texas HoldEm Poker, FrontierVille and Café World, Microsoft’s instant messenger app Windows Live Messenger is the second most popular app in this list with over 9 million daily active users.

Microsoft released the latest version of Messenger with a deep integration of Facebook and Facebook chat less than three months ago. In order to allow both Microsoft to connect its 300 million Messenger users to Facebook without running into performance issues, the two companies decided to roll this partnership out slowly. At this point, Microsoft tells us, only about 20% of Messenger users have access to it, making these numbers even more impressive.

When we talked to Dharmesh Mehta, Microsoft’s Director for Windows Live product management, earlier last week, he also noted that there have now been over 250 million chat conversations between Messenger and Facebook, lasting over 1.5 billion minutes in total. He also noted that there are just over 5 million active Messenger users on iPhones and 10 million on BlackBerry. Windows Live Messenger is part of Microsoft’s Windows Live Essentials suite. According to Mehta, 80% of new consumers PCs are now shipping with the Live Essentials pre-installed, so the user numbers for Messenger will likely continue to grow.

Update: Microsoft also just posted an update about these numbers with more details.