RealD (by far the market leader in the US - 82% market share as of today) uses a circular polarization system with polarized disposable glasses. They use a filter in front of the lens to treat the image and a light multiplier in the light engine to increase brightness. The RealD filter system, by the way, requires the theatre to install a silver screen (very expensive) so that enough light gets reflected.
Dolby (12% market share) uses reusable glasses with about 50 separate coatings on them. Instead of a filter in fromt of the lens, there is a spinning 2-color wheel in the light path. These have to be cleaned by the theatre after each use, using a wet-wipe type of towel.
Another company called Xpand (just a 1% market share in the US) uses the type of glasses you mention above. They use battery-powered reusable shuttered glasses with an infrared transmitter in the projection booth to control them (they have to flicker back and forth 144 times per second!)
By the way, I know this because it's part of what I do for a living
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