I've done this a few times and I don't have all of my information in front of me... here's what I can remember:

First off, you'll need to promote the Windows 2003 box to a domain controller. You'll first need to run adprep on the Windows 2000 Server box. adprep is on the 2003 CD (you should be able to find information on Google). This will put all of your Active Directory information on the new server.

Second, seize all of the FSMO roles from the old server. If you're not keeping the old box, the new box will take over everything.

Third, move your data. Make sure that any logon scripts are changed to reference the new server. Make sure any group policy that references the old server is changed.

Last, run dcpromo on the old box and demote it.

Understand that this doesn't include a few details... At the very least, this should give you a starting point for your upgrade.