@Yong: The be verb isn't transitive, it's stative, and doesn't take an object.Almost all native speakers of English, educated or not, will say "It was me", but if you look at 19th-century and early 20th-century grammar books, you'll see that the prescriptive rule was to say "It was I".

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In your specific case, neither 'was' nor 'were' is best; you should say "if it is running". "If it were running" is subjunctive case, used to describe hypothetical situations: "If it were running, I would stop it first, but it's already stopped."

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It does indeed mean you had that thought in the past, while watching the movie. It doesn’t automatically tell us anything one way of the other as to what you think now; and I think the natural inference without further information is that probably you still think it’s good.

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The first isn't particularly suitable for literary work. Instead of “It was then that the thought occurred to him” write “He thought” or “It occurred to him”.