I wanted to share my expierence with Getting TVersity Media Server running on a Windows Server 2003 machine.  Overall once you get the functions all working it works really well for transcoding to my Xbox 360, however the key words here are "get working".  Here's how I got it working, make sure to follow in order as it does make a difference.  First install the ACE Mega Codec Pack the link for the correct version is availble at the TVersity website, its an old codec pack but the Windows Media sections are required to make TVersity work under Server 2k3 as it lacks the encoding capabilities of other Windows Versions and FFDShow encoding crashes every time.  Only install the items to do with Windows Media Files (WMA, WMV, ASF) and skip the rest.  Next I installed K-Lite Full Codec Pack to make sure all the newest decoding filters were on the server.  I then installed the latest TVersity version and its codec pack as well.  I understand the the TVersity codec pack is redundant however unless you use it some media files seem to crash.  The final step is to open the services window (run "services.msc") and select the TVersity Media Server service.  Go to Login name and change it to "Use a Specified Account" now enter an account and password with full administrative priveleges.  You must have TVersity run with full priveleges otherwise it will crash with most media file.  Once all of the above is done you are ready to go.  Works like a charm. 

On a side note if you use .MKV or other embedded subtitles you will need some more configuration.  I will post on that in a new thread as I think that there have been a lot of people having trouble with that.