Three-act structure really lends itself particularly well to convention games, where there's a limited time frame in which to play through a given story/dungeon/scenario. I find that pretty much every game that I run at a major convention--which I've been doing for at least 10 years, plus my own home games--uses some variation on a three-act structure.
That said, there is a *lot* that a good GM can learn from alternate methods of narrative structure. I'm actually working on a series of essays designed to analyze this, focusing primarily on non-linear storytelling (such as that found in movies like Memento, Snatch, and Lock, Stock and Two Smoking Barrels).