How do you gauge which game is most popular or most fun? Is it the number of plays the game has received or its rating? Are you asking about Stencyl games on Kongregate only or on any website?
On Kongregate, the highest rated Stencyl game (if you filter out tutorials) would be Abigayl’s The Lonely Square. The one with the most plays would be Last Square Standing, also by Abigayl. If you want to see a list of all Stencyl games on Kongregate, click here.