One of the areas I found most likely to trip you up in a Windows 2003 DC upgrade is the area of application compatibility. It's really hard to know what's out there in your environment, and to plan for it. Since your domain controllers service all kinds of applications on servers in your Active Directory forest, unless you have a really buttoned-down environment, you probably don't have a handle on the apps that are touching your DC's. For example, when's the last time you talked to your network operations group about the software they use for managing their routers? Microsoft talks a good deal about Windows client compatibility, but says very little about non-Windows clients.
I'd like to hear from you - if you upgrade to Windows 20003, or you're in the middle of an upgrade, what kind of application compatibility issues have you come across?

- Sean