Chris and Trish Meyer have a good post on the gamma problem:
Brightness Issues with H.264 QuickTime Movies: Solutions - good and bad - to a long-standing problem.
They nicely summarize actual solutions, including use of a gamma stripper app from FuelFX mentioned earlier and using the x264 codec.
Update: Chris added a few details to follow up on a thread on the AE-List (Search "h.264 compression"),
The workaround Alan and Jarle mentioned works - on Windows. Which is why it didn't work for me. The procedure is slightly different inside QT on the Mac. Unfortunately, it doesn't work for playback in all apps, and has other feature and performance hits that are unpleasant (for example, it supposedly kills Fast Load).
Brian: Having a custom color profile indeed greatly aggravated the issue. Although I did still see a slight problem even with the default Cinema color profile. What is interesting is that when I switch to my custom profile (which is darker than the default Cinema profile), the untagged movies get darker as well, whereas the Apple gamma tagged movies change very little. This points further to some correction is doing under the hood - which, however well intended, is going awry in many real-world situations.
Thanks again to everyone for their suggestions. The x264 codec ended up being the way to go.