This is terrible quality video but Jessica Biel fighting vampires at the WCE Waterfront station in Blade Trinity came to mind
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Also not quite transit but maybe it should be? Jackie Chan in Rumble in the Bronx riding a hovercraft all over, from under Ironworkers bridge to right along Pacific Blvd and various other downtown streets and waterways. You don't see practical effects like this anymore.
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I saw this live in the theatre when it was new but don't remember it being this awesome. My faulty memory thought it was the seabus but no, it's an actual hovercraft.