I just finished building 2 new Quad Core Xeon servers with Server 2008 Std x64. I must say I found it much simpler to setup and get going over 2003. There's a few good improvements which you dont realize until you go back to a 2003 box.
About the only issue I've found so far is copying files between mapped drives, where sometimes it copies REALLY slowly, then bombs out - it's a known issue according to a few posts around the net. Apart from that, and the unstable Hyper-V (both the included beta and the RC0 update), it's fantastic.
A few things to be aware of if you are thinking of updating, especially if you have XP clients, is to disable AutoTuning and RSS using NETSH. Google "slow vista RDP" for the actual fix - it applies to 2008 too.