How about this - not only should you not use flash, you should turn off the image review feature! My standard procedure when I was getting on any ride, bright or dark, where I was planning to take a photo, was to turn off the image review completely, and try to set any settings that needed, err, setting, so I didn't need to fiddle on the ride.
PnS users, also, please turn off all your "noises" - your camera can work more or less silently, so set it that way when you're at WDW. The worst, of course, are the folks who, on rides like Pirates, hold their camera up high so their bright LCD is distracting, then take a photo with red-eye reduction, so there are a whole series of flashes for every photo they take. It's incredibly distracting and frustrating.
But the bright LCDs can really be an annoyance, too, which is why I turn off the image review.
Focusing can be a big problem, which is why I often used my Zenitar fisheye - everything past 2.3 feet is in focus, and it's reasonably fast (2.8), and the wide field of view means that you can pretty much point it in the general direction and it'll grab what you were looking for. In retrospect, I should have used my Sigma 28mm 2.8 as well, the infinity focus is around 12 ft which is still probably enough for many rides, but it doesn't need to have the exposure set manually like the Zenitar does.
I didn't even attempt Pirates, Haunted Mansion, or Peter Pan... maybe on a future trip. If I do, 1600ISO (or even 3200 maybe) and my 50mm at F1.4! (Or another fast lens - I'm intrigued by something like a 28mm 1.8 or 16mm 1.8 that I see are available... too bad they're pricey!) And if Pirates seems darker, it should - my understanding is that the lights were lowered after the rehab. Not only that, but the light levels have changed other times, as well. When we went in 2003, I noticed that the light levels were distractingly high in Pirates and HM - you could easily see the ceiling tiles in Pirates and the scrims in the graveyard scene in HM. As
Disneyland in 05, I noticed lower light levels and wondered if it was a DL vs WDW thing. When we went a year ago (before the Pirates rehab), the lights at WDW were lower again and the ride was better for it. I asked our guide on the Keys to the Kingdom tour and she said that they had experimented with higher light levels as a possible safety thing, hence the brighter lights in 2003, but later decided that it wasn't actually affecting safety.
So, I guess 2003 was the time to take the flashless Pirates and HM on-ride photos!
As for Carousel of Progress - we were told no photography of any kind when we went on it, so I just shut mine down. Oh well...