I made a post about a year ago regarding how some applications have a side effect of disabling Aero.  While it is still possible to create applications that have this side-effect (due to the underlying problem of applications accessing the primary display buffer directly), many of the applications that exhibited this behavior during the Beta process of Windows Vista have since been updated by their respective ISV's to no longer cause this.

The folks at Apple have done a great job specifically with updating iTunes and Quicktime prevent this problem, as well as several other Vista-specific issues that customers were hitting.  If you grab the latest versions of these applications form Apple, you'll have a much better experience.