I don't think the server path for upgrades is any better than the workstation path. It's the same core product after all. What you might have, however, well hopefully have, is less "odd crap" on the system that might trip an upgrade up.
You need to grab a practice image, possibly into a virtual machine, and test how the upgrade goes for you, see how your apps behave on an upgraded system and decide if the time taken to upgrade server, upgrade your apps, and debug is less than the time taken to build a new system and migrate across.
Oh yeah, unless you are virtualising the production machine, check the hardware is compatible with Win 2008. That would be a real nasty one.
As for a rollback plan as chopper3 suggests, thats really important too. Make sure you don't start the upgrade process until you're sure you can restore a backup of the Windows 2003 server you're upgrading.