Currently I push out Flash though GPO and everything seemingly works fine. When there is a new update for Flash I edit the GPO, right click on the existing version, choose remove and then select the "Allow users to continue to use the software, but prevent new installations" option. I will then add the new version after that. I do the advanced install and add the version number. The only thing in the GPO will be two entries for the Active X and Plug In MSIs.
I do the same thing with Shockwave and full number releases of Java and Acrobat Reader. With Java 6 to 7 I do an advanced install and have the new 7 upgrade remove the 6 version.
I wanted to see if these are the "best ways" to do this, or if "stacking" the updates is a better way to do it.