Serious issue with the .NET 3.5 installer on Windows Vista
Aaron Stebner reports an issue (some commenters call it a "nightmare") in the .NET Framework 3.5 installer that can cause a premature reboot request on Windows Vista. If the user accepts the reboot request while the framework installer or your own setup isn't completed yet, the system can end up in an unknown state.
The problem was identified in the beta of .NET 3.5, but will not be fixed in the release version. Aaron describes some workarounds to prevent this premature reboot request, and I highly recommend you add this to your prerequisite installer.