Any MSI package can be installed directly using group policy, including any Transforms that might be created. Using a tool like Orca or SuperOrca you can generally customize these MSI/MST files to do whatever setting changes you need, or in the case of applications like Java or Flash player you can use Computer Configuration->Preferences->Windows Settings->Files to deploy configuration files in the same GPO you install with.
I am currently using this in our production environments to manage Java, Flash and Reader.
How To Use Group Policy To Remotely Install Software
The major thing that stumps people is this. Installation occurs at startup, however scheduling occurs at logoff or shutdown (can't remember which). So in order for a package to get installed, the group policy that triggers the installation must have been refreshed on the local system prior to the restart that will install it. Group policy should, in most cases, be refreshing every 4 hours or so anyway, so for production this isn't usually a huge problem, but if you're not prepared for it during testing you'll simply think it's not working.