I've been having some issues with firewall and the likes concerning GPO being applied on my new 2008 DC. Is there anything that would make 2008 act differently than a 2003 server when it comes to GPO policies?
Your best bet is to create a new group policy object and edit it from the Server 2008 machine (or a Windows 7 machine, if you have one of those). I don't like the idea of installing unrequired software on a production server, but you'll have to find a happy medium between provisioning a new Server 2008 or Windows 7 machine or utilising an existing Server 2008 resource. In any case, here's the basic steps you can utilise:
The 2008 policies are just files, and they could happily live on a Windows 2000 domain controller. The important part is that they're created by a Server 2008 or Windows 7 machine. That's the key.