I have definitely noticed this too - both on a 6500/225 AND a PowerBook G3 - so it's not tied to processor speed.
The StarWars trailer (25mb version) now seems pixelated while running at thousands of colors, which did not happen with QT3. Also, when I grow the window a bit, the movie looks even more blocky and pixelated, which didn't happen under QT3 either.
Looks like they've tweaked the Sorenson codec a bit? And not for the better. I'm not getting more performance out of it, just uglier.