I am wondering on the Windows 2003 Servers I have, should I install the newest version that just came out or install the previous version? I am reading on the workstation version most people are sticking with MP3 since there seems to be a problem with MP4 on a lot of machines. Didn't know if the same was true for the server and server enterprise version.

I don't believe they have a new version of Enterprise, at least I haven't found it, but with any new product (especially Server products) you should test it first. Just because others may have had success it doesn't gaurantee you will, it depends on your environment. If you don't have a test environment or a server available for testing just test it on your own workstation with Microsoft Virtual PC or similar product in a Server VM install. I mention Virtual PC because it's free.