I have a WDW Annual Pass and have seen the Captain EO Tribute show numerous times. There is usually an announcer who does a spiel before the film starts and from what I recall, I believe it is stated that an "Original 1986 70mm Print" is used to project the show. From the many times I've seen it in the last 3 years, the film maintains a fairly clean appearance with a few speckles here and there but nothing overly distracting.
Also, if I remember correctly didn't the main ride film for Back To The Future: The Ride surface on a Laserdisc as well? I'm pretty sure that earlier YouTube videos of the ride were sourced from one of those discs, prior to the ride footage being included as a feature on later DVD and Blu-Ray releases. I can't imagine what these laserdiscs were for but there is no way they would have held up to being projected on giant screens for the ride proper. Wasn't there also one for Star Tours as well, or did video rips of that film come from another source?