Apart from reported issues in parts of CS3 with Leopard or with understanding the new Color Management, some users might have have issues with gamma changes in QuickTime renders when viewed in various applications. These sorts of problems are not related to color management in AE per se, and can manifest as luminance differences displaying the same file in AE, Shake, FCP, or QT Player.
FreshDV notes a fix in the Mac QuickTime 7.2 update, where "Apple has added a new tickbox in the Quicktime Preferences labeled 'Enable Final Cut Studio color compatibility,' with the description 'When enabled, video is not displayed using ColorSync. Source colors are read with the 2.2 gamma and are displayed in a color space with 1.8 gamma.'"
Unfortunately, gamma behavior is not consistently handled for all codecs (e.g., DVCProHD) on all platforms (or even the "visual context" of OpenGL or Direct3D in QT). Gamma tags have not always attached or read, and problems seem to be Apple's rather than something caused by Adobe's MediaCore file handling and conversion components. One issue was fixed by AE 8.0.1, because with FCP Studio 2, Apple's Uncompressed 4:2:2 10-bit QuickTime codec reads and writes pixel data differently than prior versions of the codec.
In CS3 Adobe attempted to deal with gamma changes across platforms by adding a switch in Project Settings->Color Management called "Match Legacy After Effects QuickTime Gamma Adjustments." The Legacy QT checkbox defaults to On when you open a legacy project. Generally keeping color management off and the Legacy switch on will keep things as they were in AE 7, except on Mac OS running on a PowerPC processor, where QuickTime codecs are used for some formats (including DV, 2vuy, and v210), whether or not you select Match Legacy.
Using Match Legacy mostly works fine, except when cross-platform round-tripping. Some reports have claimed acceptable gamma matches in problem situations by enabling Color Management with the project working space set to sRGB, but that could just be just for previewing files in QT Player.
There seems to be uncertainty here (from the armchair) whether the new Quicktime preference will make gamma the same in FCP, QT Player, and other apps for all codecs, but things will probably be clarified or cleared up soon for the few problematic situations.
Update: added a comment to the FreshDV article: "This preference just changes the display of movies in QuickTime Player so they match the appearance in FCP’s Viewer or Canvas. In FCP6, Apple extended the import gamma preference (User Preferences > Editing tab) to affect movies as well as stills and you can also change the gamma of a clip individually in the Browser."