Server Differences

you really need to tell us more about your needs but:
imho. in a nutshell:
2003 more secure out of the box.
2003 also current product, unlike 2000
here is some more:
http://www.microsoft.com/windowsserver2003/evaluation/whyupgrade/top10w2k.mspx

IIS 6 now uses XML for metadata
Shadow Copying (VSS)
Designed to be more secure, not everything is enabled by default as in 2000.
Supports 2003 domains.
IE 6 included