I don't know if this is still relevant or not but I'll give you my thoughts on it such as they are.
I have used Server 2008 and it is good. There are obviously differences in the set up from 2003 but nothing major from what I can remember. I was using it as a domain controller, DNS, DHCP server, web server, VPN server and it was running a mail server. My only complaint about it would be that IIS would suddenly stop working halfway through the day and the only way I could get it running again was to restart the whole thing, this happened every day for about 4 weeks before I went back to 2003. This may have been solved by now with updates.
If I remember rightly the only reason I went back to 2003 was because there was not an awful lot of support for 2008 around on the net and there was stuff that wouldn't run properly on IIS.
