I took a quick look via query.vndb.org, and the top 10 most popular engines in terms of releases are Ren'Py, KiriKiri, TyranoScript, Unity, NScripter, LiveMaker, RPG Maker, YU-RIS, Flash, and Artemis (from most to least).
This is of course not an exact ranking, since the same game can have many (nearly identical) releases, but it roughly matches my experience
This is of course not an exact ranking, since the same game can have many (nearly identical) releases, but it roughly matches my experience