Clapping is just a way of expressing your enjoyment. Not something I'd do, but nothing wrong with it, even when the people responsible aren't there.
Mind you, The Avengers is the type of film best enjoyed with a large, loud audience. It's a great film, but certain parts were enhanced by the audience reactions. No clapping, but lots of laughs and cheers. One moment in particular was the loudest I've ever heard a cinema, and I wouldn't have it any other way. Anybody who's seen the film probably knows which bit I mean.
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^Poorly disguised anti-caps sig